As you might guess from my name, I run games online and love it.
I first tried a program called OpenRPG, then discovered gametable, then discovered MapTool. Since then, it's been all MapTool and I've loved it.
I did some demos of other systems at GenCon, and the one that looked the most tempting is Fantasy Grounds, but I honestly don't see a compelling reason to switch away from MapTool and Skype.
If you want some education on using MapTool, you can look at the
MapTool Education Central section of my blog. There are also
great videos out there about learning to make maps and such in MapTool. There are some pre-built frameworks for various games that make things easier to run, although those are overkill in a lot of cases.
I'll also say that for simplicity, don't worry about lighting and vision-blocking layers. These are features that MapTool does especially well, but I find them to be overkill. You can have "fog of war" covering the sections of map that you don't want the players to see yet, and then easily remove the fog as they explore new areas. That's enough - don't worry about vision-blocking layers.
Welcome to online D&D!