Once the basic disassembly has been generated, I annotate it with "comments" as I perform my "by hand" analysis. I use vim and do lots of searches.
I have written a handful of python scripts to clean up things that I find annoying. As any sensible person ought to do, when I find myself performing some tedious simple repetitive task, I think about writing a program to automate it.
One tool I am particularly pleased with is one that finds all mrc and mcr instructions and replaces the meaningless junk with sensible mnemonics.
Tom's Computer Info / tom@mmto.org