I vary. Mainly phasers for most of my Fed ships, though my Wells uses AP, my Jem Dread uses Phased Polaron, my Recluse uses Phased Tatryon. I've got a Protonic Polaron/Proton build planned for the Science Destroyer.
I like Nanite Disruptors, Disruptors and Plasma weapons on my Romulans, though I have a Haakona fitted with Phasers and a Mirror Ha'apax with Polarons.
On Klinks - anything goes. I've got Spiral Waves on my Engineer's Bortasqu, and AP beams on my Sci's Vo'Quv and upcoming Nov.