Dungeon Mastering has an article on tools to make your life easier when running or playing RPGs online. It’s very useful, though I feel it only briefly touches upon some of the tools that are out there. The nod to Skype is definitely one I agree with, as our group uses it for our weekly games (Trail of Cthulhu at the moment).
In particular, the Battlemat section is very thin. Maptool and Gametable are solid mentions that I can definitely agree with, but if you’re willing to spend a few dollars, then I would highly recommend Fantasy Grounds 2, which is what our group uses. It’s a bit more directed at particular systems (D&D 3e, Savage Worlds, BRP Cthulhu), but with a bit of digging, you can find some useful fan-made system plugins. In particular, being so focused, it requires a bit less effort to handle maps (with obfuscation layers to boot!) and miniatures.
In any case, check out the article at Dungeon Mastering.