I have done a quick and dirty wikification of this very useful thread:
http://wiki.spaceempires.net/index.p...#Modding_Tools
Please feel free to update it as you post here (because I probably won't do it) and to be honest each of the tools listed here should probably have its own wiki entry.
EDIT: Just to labour the point I've made a wiki page for Matryx's mod launcher. It's not very pretty though, someone cleverererer than me might want to tidy it up:
http://wiki.spaceempires.net/index.php/Mod_Launcher