All my notes are just bookmark files from Hex Workshop.  My directories are pretty disorganized, although I usually limit the types of roms to one per directory.  That means my NES roms are sepereate from the SNES, but the NES roms are in with the emulator, while the SNES roms arn't.  I also have backups of backups of backups, and I rarely get to delete them all.  It's all a mess, but it's comfortable and I am rarely without what I need.  I also hand code ASM hacks in the hexl editor, so no need for disassembly tools.  My hacks in general arn't planned out, and it just spawns from an idea and goes from there.  That's the secret to having half finished, outdated projects that collect dust before being released as imcomplete hacks.