STO fully compatiple,
Yaki Armada and Pirate Guild should be fully compatiple, just ask the forums known privateers .
Anarkis should be compatiple too.
MARS as pointed out, needed a little bit of tinkering, iirc.
Khaak Invasion isn´t really needed, as you can configure them through the XTC config menu. Same goes for Xenon.
RRF, no clue.
Custom Wing Manager should be fully compatiple.
Reduced enemy Missiles count, idk.
as for ATF Shipyard: didn´t the ATF SY Script come packaged with a pair of cat/dat, if so, stay away! Otherwise you might have to tweak it here and there.