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This is variable depending on the species of reptile and the type of environment bet for that animal. And even then is highly debated at times between experienced keepers. The standard options are:
Cypress mulch: Very good at holding humidity. Not great to burrow in. There are people who are concerned that they may get mites from this coming from a home improvement/garden center. It is highly unlikely, but there is a god chance of it having insects of some form. The simple cure is, get a new clean large trash can, put the mulch in, make sure there is 6" or more of space above the substrate. Hang a No Pest Strip in the can and close it. Leave it for a week or more, stirring it every few days.
Fir bark: From the bark of fur trees. It is sold in pet stores as "repti Bark" and a few other brand names. Sold for 5-10% of the price at garden centers as Orchid Bark. Use the same system as above to treat for insects if you are worried, but it is normally dry and tightly sealed, as it is intended for indoor orchids.
Compressed Coconut Fiber: I love this stuff. It is shredded coconut husk, sold as a compressed block. Add a little water and it opens up. Can be used wet or dry, hold humidity very well, is great for burrowing and burying eggs. Sold in pet stores as "Eco Earth" and a few other brand names, you can also get it at some garden centers, or anywhere that sells indoor gardening or hydroponic supplies. I love this stuff.
Sphagnum peat moss: Very good substrate for some things, can be messy when kept wet. Personally, I don't really like it.
Sand: I don't like using this as a primary substrate for most animals. It is very hard to keep sanitary, and grows bacteria wonderfully. It is easily ingested by smaller insectivorous lizards. I do use it in separate boxes inside my bearded dragons enclosures, for digging. But it is easy to change out and closeable when feeding if miscarry.
Newspaper/paper towels: Cheap, efficient and sanitary. Not pretty, but it works. In enclosed environments it can be kept moist for humidity. Very easy to clean.
Doggie training pads, Bed liner pads: Seriously. There are great for enclosures that need higher humidity, for emerald tree boas, green tree pythons, etc... Can hold a good deal of water and release it slowly.
Vinyl flooring: My choice for arid environment reptiles. Easy to clean, easy to cut to fit, fairly cheap and lasts a long time. Get the type without the adhesive backing, that can give off fumes when kept warm.
There are others, people using all kinds of things, like eucalyptus mulch, because it is insect resistant, potting soil, etc... And for any who don't know, never use any oily aromatic soft wood, like cedar or pine, especially not cedar. They can cause severe respiratory infections in reptiles
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