This is a work in progress!
Be sure to post the tools you use in the comments :)
Windows Tools
LS1 Flash Tool - Still in development, but you can tell it has a future here.
TunerPro - Has ability to tune and scan, a must have.
WinOLS - Great program, hex editor, has a 2D and 3D view, and more. Great for locating maps in a binary.
HxD Hex Editor - Hex editor.
wOBD - This is a great tool, sadly last update is from 2006. Still a great app, say you want to poll every pid at $22, $3C? This is it.
IDA - Disassembler and debugger.
DISMOT68 - Two pass Motorola 6833X disassembler. Support definition files and structure.
STNTerm - Terminal for ELM and STN.
OS X Tools
Synalyze It! - It's the best hex editor I've used. You can make configs called grammar, highlight bytes, label them and a ton more. Make sure to try the grammar that is provided with the program, pretty neat stuff. Here's a bin I just started working on...
CoolTerm - Well this one is cross platform but only tried OSX version. It has support for AppleScripts, and works great.
Wine - It lets you run Windows programs on OSX.
Linux Tools
Bookmarks