I play Proportions mod only, so my list
is for that mod:
Favorite : Torpedos. PvK made them usefull
and I simply like the sound they made.
Uuooghhh... Uuooghh... or something
Shield-skipping Graviton Hellbore in Prop2.5
is my second favorite.
Useless: Direct-fire Organic weapons. PvK left them as in normal SE and with all those changes to other weapons Organic' are very weak. Seeking Parasite is the only worthy organic weapon now
PPB are almost useless too - research cost is very high.