IDA Pro is the best tool I know of for doing this. It's pretty expensive, but has some features that speed up renaming things, cross-referencing, and navigating around in the code. It also has a scripting feature that helps a lot, for example I turned an XDF file into a script that labels all of the constants and tables in my 2002 Corvette's bin file, which gave me a good head start.

I'm keeping my IDA file on GitHub, and I've also posted a few things in a wiki there:

https://github.com/LegacyNsfw/12593358

I've barely scratched the surface, but it's a start.