Douglas Cole (Gaming Ballistic) started off a chain of excellent blog posts on other blogs with his post on using virtual table top systems to game online. I have used three systems: Gametable, Fantasy Grounds II, and Roll20.
Gametable: Gametable is a very simple Java-based program, which will be an issue for Java haters. I think Gametable works works great for dungeon-based play, particularly sessions involving dungeon exploration. Just start with a blank graph screen and draw the rooms and corridors as the players explore. I can draw a map from scratch in Gametable faster than I can reveal a prepared map using the fog-of-war function in other VTT. Gametable is great for those who do their mapping on graph paper...no need to create an electronic map ahead of time. Just draw a map for the players as they explore. Gametable is not pretty, but its simplicity reduces glitches. Because the GM's computer is the host server, port issues can be a significant challenge.
Fantasy Grounds II: Very pretty and feature rich. The fact that the GURPS rules are built in makes it my go-to VTT if I run a GURPS campaign. The GM is the host, so it has the same port issues as Gametable but I think Fantasy Grounds is easier to set up. The high amount of data transferred back and forth can make it glitchy, plus it can interfere with Skype or Google hangout conversations.
Roll20: Just log-in, set up a web-based campaign, and then invite your gaming group. The GM does have to upload maps and such, but that is easy to do. It is not a pretty interface and it is not always obvious how to do things but the instructions are helpful. We are currently using Roll20 for the Montporte Dungeon campaign.