Wow, two year old thread. Very nice. I voted for AP, but also use plasma and disruptors. Honestly, the mods matter more than weapon type. For instance I'd much rather a plasma crtdx4 than a fleet AP. All other things being equal though AP is still king because of the extra crtd mod.
I like to broadly keep things canon. I use phasers on my Federation ships (usually Andorian as my character is Andorian). On my Tholian Recluse I use Tetryon and on my Voth Bastion I use Anti-Proton. I mainly stick to genuine fed ships though.
For DPS I'm sure I should really change to AP or Disrupter etc. but my DPS seems fine on Advanced STF's
Val: plasma beams
Akima: phaser cannons
Nadine: Herald AP beams
Karoni: Disruptor beams
I use Andorian Phasers because my OC is an Andorian Supremacist who believes only Andorians can save the Federation in this era of constant war - so naturally his phasers are Andorian. Even though it might not be the most powerful build using the Fleet ones is does OK.
I am very tempted to do a Vaadwaur Polaron build though - just don't have the EC for it at the moment.