I would like to know what people think the best weapon setup is for STF's..
Space and Ground !
I'm interested in what people have found works best..
Well for ground STFs you'll want, at the very least, the Veteran Maco or Omega set. It has an Antiproton weapon which is pretty good. I also recommend a Pulsewave Assault Rifle (I suggest any energy type besides Antiproton since the Maco/Omega weapon is already Antiprton). I use the Omega set, and what I like to do is have the Omega weapon as my secondary weapon and my Pulsewave as the primary weapon.
For space, a lot of people like Antiproton weapons but in reality it doesn't matter. The only thing I would suggest is getting the weapons that have the [Borg] trait. These are obviously better against the Borg than other weapons.
I use Antiproton beams and cannons and Quantum torpedoes, but also in your tactical slots use devices for your weapons that will increase your damage to opponents. Also good shields and insulators, since the Borg love to drain your shields. This is what I have been using and although I have been hurt pretty bad, but my ship survives.
Peter are you in the fleet? If so then check the STF Squad section of the fleet forums for all your space related questions, or hit me up in game if you can catch me on.
To briefly answer your question, as it really would take a lot to answer and i don't want to repeat what I have said elsewhere in length if you can just view that section, it depends a LOT on what role you are filling in the STF.
My Dreadnought, which fills the Flagship role, is set up to do massive DPS and have a very strong tank. My Science character, once I get him up to spec, is going to be set up with a Caitan Carrier which is set for CC and or Healing depending on the rest of the groups composition. My Gorn is in a Carrier set up for CC/DPS/Guard duty. Each of these set ups have different needs.
As to best weapon, there isn't one, though many people will say Antiproton. The reason for this is that each energy type has the same chance for its effect to go off as the other types. The exception is Antiproton which has increased crit chance instead of a secondary effect. You also have to look at what other things you have that may matter. For instance my Dreadnought is Phaser for two reasons, first because I use Quad Phaser Cannons and Point Defense System on it, and second because of the Spinal Phaser Lance. All three of those items all gain increased damage as a phaser type weapon so it makes the most sense to have my other weapons be phaser also.
Only hard rule for weapons is have them all the same type for Energy, i.e. all plasma or antiproton, and the same type for projectile, i.e. all quantum or photon.