JDGUI by itself is usually sufficient. Most mods don't obfuscate themselves, so you're left with only the Minecraft obfuscated parameters, but most you can figure out just by the context, the rest you can lookup using MCP
I actually peeked inside Twilight Forest at the Anti-Builder to see if it had done anything special/clever to minimize get, save, check, and reset blocks (as I needed similar functionality). It was just a standard 3 dimensional for loop. I've also poked my nose into Mystcraft on occasion (notably when trying to figure out how to use XCompWiz's API, I'll get confused over the usage of one parameter, so I pull up base and take a look at how he was using it).