At the moment:
COFH Lib
Ex Nihilo
MicoodleCore
Industrialcraft API
SuperCraftingFrame
StevesAddons
Morpheus
StevesAddons
InfernalMobs
Those are the ones that I can remember - some are just versions and others are both versions and names.
The other issue I am running into is it seems to just be ignoring half them. The end result of running it left me with 33 out of 209 mods actually compiled into the folder.
Thoughts?