Okay... Let's see this...
Guerilla:
Kol Frame: For obvious reasons...
Colonization (Progenitor): quick expansion
Missile Barrage: for VERY obvious reasons...
Stabilize Phase Space
Raze Planet: combine with the above to have the best guerilla ship in the game...
Combat:
Kol Frame: duh...
Missile Barrage: fleet killer
Cleansing Brilliance: cap killer
Malice: combine with above for fleet killer
Flux Field: makes repeated use of the above viable...
Super-Hoho:
Dunov Frame: because it can...
Shield Restore: for mass healing
Repair Cloud: for mass healing
Ion Bolt: for so many purposes
Energy Absorptive Armor: so you can use the above attacks
Destructor:
Amplified Targeting Aura: increases range
Finest Hour: decreases cooldowns
Flux Field: see below...
Missile Barrage: combine with the above, and you will have a ship that will love plowing through your fleet...
Planet Bomber:
Provoke Hysteria: for killing those big annoying planets...
Siege Specialization: obvious reasons
Raze Planet: obvious reasons
Drain Planet: obvious reasons
Nuff' said...