Used Roll20.net to start a new D&D campaign with my sister and her husband that live half way across the country. Previously we used MapTools, but I'm happy with the switch.
MapTools does two things better: it has a much more robust macro system, and you can create prettier maps using the tile system. Roll20 has macros, but they don't have the power to write information. They can only read variables and output the result of equations. And while you can import pictures and tiles, it's very hard to manage large amounts of objects with the roll20 interface. Better to keep things simple.
But Roll20 has a bunch more advantages. It's all browser based so there's no need to download an application. There's also no connection issues when trying to get everyone into the same game. Webcam and voice are built in to roll20 so you don't need something like Skype running in the background. The interface is also more user friendly, especially for those who aren't so tech savy like my sister and brother in law. And my favorite feature: 3d dice that roll on everyone's screen. Much more fun than a random number appearing in a text box, and much harder for the PCs to fudge roles if we use real dice.