Selecting the Substrate
It is best to use a calcareous substrate such as crushed coral or dolomite. These substrates will, at least initially, help buffer the water by adding ions to the buffering system. Generally the substrate should not be so tiny as to get sucked into the filter or pumps, and not so large as to make the tank unsightly. Also, some fish (e.g., Gobies) like smaller grades of substrate over larger ones. Something in the 2-5mm department seems average.
Live sand is one substrate which has recently gained a fair amount of publicity. This technology is really in its infancy and is not recommended for beginners. You can find more information in the ARCHIVE.
Filtration System
After you select a substrate, consider the filtration system you plan to use. Your choice in filtration may impact the amount to substrate you need. A UGF or RUGF filter should have about 2-3" (5cm) of medium grade (2-3mm) substrate covering the filter plate. You do not need substrate when you use non-UGF filters (e.g., hang-on-the-back power filters), but, most people use between a 1/2" to 1" for such tanks. It's interesting to note that too much substrate in a non-UGF system might lead to dead spots, which can kill your inhabitants (a plug for regular gravel cleaning).
