Here I will be going over some of the most commonly used substrates in the hobby.  I will be giving them ratings based on safety, price, ease of cleaning, how naturalistic it is, reptilian preference, and overall use.  Before deciding on a substrate research the animals particular needs and habitat; not all substrates, even good ones, work well with some species.

(Remember these are opinions formed from my personal experience with the substrate; most are described for the use on snakes, so some may be different in regards to other reptiles.)

 The substrates:
Aspen shavings, Bark (Reptibark, coconut bark), Calcisand/vitasand, Carefresh, Carpet (repticarpet/Astroturf etc), Cedar shavings, Coconut fiber (Eco-earth/bed-a-beast), Crushed walnut shells (Desert Blend Lizard Litter), Cypress mulch, Gravel/rocks, Moss(sphagnum, peat), Newspaper/butcher paper/cage liners, Paper towel/napkins, Pine shavings, Playsand, Soil, Tile. ~ Outcome

Aspen Shavings
A soft wood usually shaved or shredded; used commonly for rodent bedding, sold often compressed in bags in small animal sections of pet stores.

Safety -  As with all loose substrates aspen poses a risk of ingestion, so caution is needed.  To reduce the risk feed out of the enclosure, on something solid in the enclosure, or wait for the snake to be of good size to handle pieces in case of accidental ingestion.  Aspen is a soft wood, and can most of the time pass easily through the snake, as well as posing little to no risk for slivers or other wounds.	Rating:  3/5 Stars
Price - Decently priced depending on where you look; check out places like Walmart or farm supply stores for larger bags at low prices compared to pet stores.	Rating: 4/5 Stars
Ease of cleaning - Easily spot cleaned, and a wonderful deodorizer; complete substrate changes being needed once every other month to every few weeks depending on the size of the snake.	Rating: 5/5 Stars
Naturalistic - Fairly natural looking; simulating leaf litter.	Rating: 3/5 Stars
Reptilian preference - Snakes, especially ones that burrow, love aspen.  Its very easy to burrow in, and it holds their tunnels which they will re-use.  It does mold easily though, so should be avoided for species that need higher humidity.	Rating: 5/5 Stars
Overall - The substrate of choice for most colubrid keepers; this is one of the best substrates for species like corns, rats, kings, and milks.	Overall Rating: 5/5 Stars

 

Bark (Reptibark, coconut bark)
Large or small chunks of bark; dark brown/red, often dyed.

Safety - Pieces can be ingested, and can cause more problems due to their size and hardness, as compared to softer wood shavings.  Rare cases of giving slivers too.	Rating: 2/5 Stars
Price - Somewhat expensive; I wouldn't recommend it for use with big enclosures, where you may need to replace a whole bag every time a large snake defecates.	Rating: 2/5 Stars
Ease of cleaning - Simple spot cleaning is needed.	Rating: 3/5 Stars
Naturalistic - Very natural looking, its dark browns and reds accent jungle and forest type setups	Rating: 4/5 Stars
Reptilian preference - The chunks can be quite hard and rough, nor do they allow burrowing very well.  Even snakes I have found have a preference over what they lay on, with reptibark being quite uncomfortable (I have even heard of snakes refusing to rest on it, spending their time in branches, on hides, or in water dishes instead).  Also if when wet they dyes from the wood may stain the scales of the snake.	Rating: 2/5 Stars
Overall - While it looks great in many setups, when it comes to the snakes there are better choices out there; especially for that price.  One option though is it use it mixed with other substrates such as soil or coconut fiber, which seems to work pretty well.	Overall Rating: 3/5 Stars

Calcisand/vitasand
Sand made from calcium and minerals, available in different colors.

Safety - Easily ingestible; due to it being digestible the particles hang in the stomach instead of passing though, however they are digested slowly forming jagged edges where each piece may lock together with another and can slowly form a blockage.  Can also get stuck in nostrils, mouths, heat pits, vents, and under scales.	Rating: 1/5 Stars
Price - Rather expensive, not recommended for larger enclosures.	Rating: 2/5 Stars
Ease of cleaning - Spot cleaning or sifting with cat litter or specially made sand scoopers.	Rating: 5/5 Stars
Naturalistic - Can look nice in desert type enclosures; the different colors available can add an interesting touch.	Rating: 4/5 Stars
Reptilian preference - Very few snakes in captivity actually spend all their time on inches of loose sand, even those from desert climates are on very compact earth and rocky surfaces.  Sand is not a natural substrate for all but a few snakes, and because of that most snakes arnt designed to live on it.  It can be hard to burrow in, is very drying, and can make it difficult to maintain appropriate temperatures.	Rating: 1/5 Stars
Overall -  While it looks nice and is easy to clean, calcisand/vitasand is in fact a very poor choice as a substrate for most snakes (and most lizards too).  Add that to the fact that it can and has caused impaction and death in snakes and lizards it is one substrate I don't recommend even for species that do live on sand (regular smooth grained play sand is better).  A safer alternative is tile with a light layer of sand on top.	Overall Rating: 2/5 Stars

 

Carefresh
A recycled newspaper litter made for small mammals.

Safety - A risk of ingestion, but fairly easy for larger snakes to pass.  Can also be somewhat dusty.	Rating: 4/5 Stars
Price -  Higher priced compared to other substrate options.	Rating: 2/5 Stars
Ease of cleaning - Spot cleaning with total substrate changes every few weeks to every few months, depending on the size of the snake.  Absorbs liquid and deodorizes.	Rating: 5/5 Stars
Naturalistic - Not very attractive looking.	Rating: 1/5 Stars
Reptilian preference - Soft and great to burrow in.	Rating: 4/5 Stars
Overall - Its price doesn't work well with its looks, however it works great for many snakes, especially those who like to burrow.	Overall Rating: 4/5 Stars

Carpet (repticarpet/Astroturf, etc)
Flat pieces of either specially made reptile carpet, Astroturf, indoor/outdoor carpet.

Safety - Since they are solid pieces ingestion is very rare, but there is still a very small chance of a tooth getting stuck while eating.  For lizards there is also a chance of toes getting stuck too.	Rating: 4/5 Stars
Price - Not too expensive and is re-usable.	Rating: 4/5 Stars
Ease of cleaning - Can be a chore to clean; scrubbing, soaking, and drying; and it still will probably not be totally clean. A couple pieces on hand are a great help, to keep rotating while one is cleaned and dried.  Bacteria is easily trapped in it, and after awhile they can start to smell.	Rating: 1/5 Stars
Naturalistic - Somewhat naturalistic, but not the top looking choice.	Rating: 3/5 Stars
Reptilian preference - It doesn't allow for burrowing, unless they find a way under, which usually isn't desirable.	Rating: 2/5 Stars
Overall - A better looking alternative to newspaper, however the cleaning gets old fast.	Overall Rating: 3/5 Stars

Cedar Shavings
Shavings of a harder fragrant red wood.

Safety - Cedar has a strong smell, which is from its oils.  Those oils are highly toxic not only to reptiles but small mammals as well.  It is dangerous and should be avoided at all costs.	Rating: 0/5 Stars
Price - Not bad, usually comes in bulk as mulch or for dog beds.	Rating: 3/5 Stars
Ease of cleaning: - Spot cleaning, with total substrate changes when needed.	Rating: 3/5 Stars
Naturalistic - The color is nice, but it looks less natural then other mulches out there.	Rating: 2/5 Stars
Reptilian preference - Do not use this substrate for reptiles, if they are kept on it long enough it will kill them.	Rating: 0/5 Stars
Overall - I cannot say it enough - Cedar kills - Snakes I have known that were kept on it (through owners ignorance) developed severe neurological problems when on it even less then a month.  Once off it they slowly recovered, however not 100%.	Overall Rating: 0/5 Stars

Coconut Fiber (Eco-Earth/Bed-A-Beast)
Coconut fibers, shavings, grounds compressed into a brick that has to be soaked to expand then dried for use.

Safety - Fairly easy to be ingested, but small pieces usually pass easily.  It has a tendency to stick to things when when, and can easily get stuck in mouths, vents, nostrils, heat pits, etc.	Rating: 2/5 Stars
Price - Not bad for the amount once expanded.	Rating: 4/5 Stars
Ease of cleaning - Spot cleaning is extremely simple, however total substrate changes take awhile, as a new block has to be soaked then dried before use, which can take a day or longer.	Rating: 2/5 Stars
Naturalistic - One of the nicer looking substrates, mimics a forest floor nicely.	Rating: 5/5 Stars
Reptilian preference - Easy to burrow in and is generally soft, however usually very gritty and sticks to anything wet.  Hold humidity well though.	Rating: 4/5 Stars
Overall -  A nice alternative to wood chips/shavings, and beneficial to species needing humidity, however can be a real mess to deal with and time consuming. It is usually the most common substrate used in mixes, mainly with bark or mulch.	Overall Rating: 3/5 Stars

Crushed Walnut Shells (Desert Blend Lizard Litter)
Ground up walnut shells, looking like large grained sand but softer then sand.

Safety - The large grains are rough and sharp, and easily ingestible making the potential for problems.  Can get stuck in mouths, vents, nostrils, heat pits, and under scales.  Reports out there show a slight toxicity, however so far it only seems to be with fish.	Rating: 2/5 Stars
Price - Decent sized bag for the price.	Rating: 3/5 Stars
Ease of cleaning - Spot cleaning, with total substrate change when needed.	Rating: 4/5 Stars
Naturalistic - There are better looking desert type substrates out there; it looks more like a litter then it does sand.	Rating: 2/5 Stars
Reptilian preference - Quite abrasive; very few desert species actually live on a loose substrate like this like with sand.	Rating: 1/5 Stars
Overall - If your going to use a loose substrate for desert species go with play sand instead of this, it really isn't a good substrate.	Overall Rating: 1/5 Stars

Cypress Mulch
Light to dark brown shredded mulch.

Safety - Cypress is a harder wood, and often in longer chunks; so it is more dangerous if ingested compared to other woods out there, however it does tend to lock to other pieces making a more solid flooring rather then loose pieces.  Be sure it isn't chemically treated or anything.	Rating: 2/5 Stars
Price - Great price, found at garden supply stores in large bags; perfect for larger enclosures.	Rating: 5/5 Stars
Ease of cleaning - Spot cleaning, with total changes when needed.  Some bags carry little white wood mites and other bugs, which mostly are not harmful to the reptile but still a nuisance, so baking or freezing the wood may be needed.	Rating: 3/5 Stars
Naturalistic - Very nice looking, great for forest and jungle type enclosures.	Rating: 5/5 Stars
Reptilian Preference - Harder to burrow in, so not really recommended species that like to burrow; but is a great ground cover for larger snakes, it isn't too rough and is much softer then newspaper or bark.  Its an excellent humidity holder, one of the best choices for those with higher humidity needs.	Rating: 4/5 Stars
Overall - A great looking affordable choice for jungle dwelling snakes with humidity needs, and large bodied boas and pythons.	Overall Rating: 4/5 Stars

 

Gravel/Rocks
Colored aquarium gravel, natural gravel, aquarium/river/landscaping rocks.

Safety - While more difficult to ingest, there is a great chance of problems being caused it a piece was.  Rougher pieces your asking for scale abrasions too.	Rating: 2/5 Stars
Price - Decent priced, depending on what kind.	Rating: 4/5 Stars
Ease of cleaning - Difficult to clean fully, unless dirtied spots are disposed of instead of washed.	Rating: 2/5 Stars
Naturalistic - Aquarium gravel, while the colors may be fun, in no way accents the enclosure as whoever looks at it knows that it is aquarium gravel.  Other gravel and rocks may look nice, however they work much better as details, not as the main substrate.	Rating: 2/5 Stars
Reptilian Preference - By far not a good choice for any species; very uncomfortable, impossible to burrow in, can cause heating problems.	Rating: 1/5 Stars
Overall - A very poor substrate choice, not recommended at all.  Is fine in small amounts with a more appropriate substrate, but should never be used alone.	Overall Rating: 1/5 Stars

Moss (sphagnum, peat)
Vegetation, often dried, comes in long strands, clumps, or ground.

Safety - Can be ingested, but is soft and can be easily passed.  Can draw in bugs when moist, and can also cause scale (blisters) problems when kept too moist on some snakes when forced to spend all the time on it, and some is prone to molding.  Can be very dusty when dried.  Be sure there are no chemicals or fertilizers in it (organic).	Rating: 4/5 Stars
Price - Moss sold for reptiles can be expensive, but its usually pretty cheap at garden stores.	Rating: 3/5 Stars
Ease of cleaning - Spot cleaning, however can be a hassle if it's in large masses, as sphagnum usually is.	Rating: 3/5 stars
Naturalistic - Can look very nice in tropical enclosures.	Rating: 4/5 Stars
Reptilian preference - Easy to burrow in, very soft, but not very solid normally.  Great for humidity	Rating: 3/5 Stars
Overall - It takes a lot, especially of the compacted clumped sphagnum, to make a solid floor, it does much better as an accent over another substrate and in humid hides then as the main substrate.	Overall Rating: 3/5 Stars

Newspaper/Butcher paper/Cage liners
Flat sheets of paper, printed or unprinted, cut to size or not.

Safety - Very safe, flat sheets nearly impossible to ingest, but it has happened on the very rare occasion.	Rating: 4/5 Stars
Price - Very cheap, if not free.	Rating: 5/5 Stars
Ease of cleaning - A little more work then spot cleaning, but still easy; just roll up and throw.	Rating: 4/5 Stars
Naturalistic - Not natural looking at all.	Rating: 2/4 Stars
Reptilian preference - Little cushioning; burrowers find ways under the paper, which ends up making a pretty good hide, although frustrating when it comes time to take them out.	Rating: 3/5 Stars
Overall - One of the most commonly used substrates, its price, availability, and ease of cleaning easily make up for its lack of good looks.	Overall Rating: 4/5 Stars

Paper Towel/Napkins

Safety - Flat sheets make it nearly impossible to be caught while eating, but there is still the very rare occasion it does get caught.	Rating: 4/5 Stars
Price - Better quality is going to be more expensive.	Rating: 3/5 Stars
Ease of cleaning - Just roll up and toss; highly absorbent.	Rating: 4/5 Stars
Naturalistic - Not natural looking, but a bit better on the eyes then newspaper.	Rating: 3/5 Stars
Reptilian preference - Same with newspaper; soft and makes a nice hide to burrow under.	Rating: 3/5 Stars
Overall - Basically the fancy alternative to newspaper, with the price often reflecting it.	Overall Rating: 4/5 Stars

Pine Shavings
Shredded or shaved pine wood.

Safety - The usual ingestion risks.  Pine has been shown to be slightly toxic, not at the severe level that cedar is; however in studies done on small animals over time the toxins build up in their system.  Many have used pine without no visible problem, but I wouldn't suggest it when there is aspen, the safer alternative, is available.	Rating: 1/5 Stars
Price - Decent; larger bags from farm supply stores and some pet stores are well priced.	Rating: 4/5 Stars
Ease of cleaning - Spot cleaning, with total changes when needed.	Rating: 5/5 Stars
Naturalistic - Not bad looking, but only does a little to enhance an enclosures look.	Rating: 3/5 Stars
Reptilian preference - Simulates leaf litter, holds shapes of burrows well; but the toxicity doesn't help.	Rating: 3/5 Stars
Overall - Another substrate where there is no need to purchase due to a better alternative, without the toxic properties.	Overall Rating: 2/5 Stars

Playsand
Smooth small grained sand used for sandboxes and such.

Safety - Easily ingested, but passes through easier then other sands making less of a risk for impaction (but there is still a risk of it).  Can get under scales, in mouths, vents, nostrils, heat pits.	Rating: 2/5 Stars
Price - Good price when bought in large bags; smaller bags made for reptiles are more expensive.	Rating: 4/5 Stars
Ease of cleaning - Spot cleaning/sifting is most thats needed, with complete substrate chances occasionally.	Rating: 5/5 Stars
Naturalistic - Looks quite natural for desert type enclosures.	Rating: 5/5 Stars
Reptilian preference - Most reptiles, even desert species, don't live on inches of loose sand, however if that route is taken play sand is the best choice.	Rating: 2/5 Stars
Overall - The safest sand out there, if sand is used make it play sand.  Remember though - only use it for the species who are designed to be on sand, never ones that arnt.  A safer alternative is tile with a light layer of sand on top.	Overall Rating: 3/5 Stars

Soil
Soil or dirt used for gardening.

Safety - The biggest concern is to not use any with added chemicals, pesticides, fertilizers, etc; organic and untreated pure soil is what you want.  It compacts nicely so its harder to get stuck in mouths, vents, nostrils, heat pits, and scales.	Rating: 3/5 Stars
Price - Depends on the brand.	Rating: 2/5 Stars
Ease of cleaning - Spot cleaning, however total changes can be more work then other substrates.  It does often however have the ability to naturally break down any waste as it would in the wild, but setting it up and maintaining it for that can be a lot of work.	Rating: 2/5 Stars
Naturalistic - Very nice looking for many type of habitats.	Rating: 5/5 Stars
Reptilian preference - One of the most natural substrates out there; have to be careful though for many reptiles prefer not to be stuck on moist dirt all the time.	Rating: 4/5 Stars
Overall - It can be a challenge finding 100% chemical free organic soil.  Those using it also include plants and other things to make a very nice setup, so with its nice looks comes a good amount of work to keep looking nice.	Overall Rating: 3/5 Stars

Tile
Slate, ceramic, or vinyl.

Safety - Very safe, no risk of ingestion or injury (if there are no sharp corners).	Rating: 5/5 Stars
Price - Depending on what type and where its got; its generally pretty affordable.	Rating: 4/5 Stars
Ease of cleaning - Just wipe clean.  Total cleanings while usually not needed can be a bigger task though.	Rating: 4/5 Stars
Naturalistic - Many available options out there; slate being the best looking.	Rating: 4/5 Stars
Reptilian preference - For most desert species its more natural then sand.  You do have to watch the warm side closely though, slate and ceramic absorb heat almost too well.	Rating: 4/5 Stars
Overall - Setup can be a chore, needing to break or cut the pieces to size; but once set up these enclosures often are much closer to most desert species natural habitat.  Fill in the cracks and out a light layer of sand on top and you've got a great desert enclosure without the risks sand brings.  I suggest not permanently affixing it to the floor of the cage.	Overall Rating: 4/5 Stars

 

 

Outcome

Aspen Shavings
Carefresh
Cypress Mulch
Newspaper
Paper towel
Tile
Bark
Carpet
Coconut Fiber
Moss
Playsand
Soil
Calcisand
Pine Shavings
Crushed Walnut shell
Gravel/Rocks
Cedar Shavings