No, seriously. Pick the weapon type that you most prefer based on any set bonuses you may have (i.e. Jem'Hadar boosts Polaron) or based on which proc you prefer most (phaser: disable subsystem, tetryon: reduce shields, etc).
For STFs, though, you'll want at least very rare mk XIs, an you'll want to maximize your effective damage output. That means take all one type (phaser, tetryon, whatever you like) and maximize your consoles so that you get the most boost for that type.
This also means maximizing your boff setup so that you can survive and do damage at the same time. For escorts this means damage-dealing skills. For cruisers, repair or healing skills, etc.
STFs aren't about any 1 type of weapon as much as an overall effectiveness that you need. Work the borg sector encounters first to test your capabilities. Then when you're able to do that move on to NORMAL STFs. NOT elites. NORMAL first. Don't screw up the games at elite level for others until you know what to do.
So overall: It's about not screwing things up for the folks that are looking for serious borg tech drops. If you die too much you're screwing the team over. If you're not doing as much damage as your particular build can, you're screwing your team over. If you're not working to the mission goals and pitching in, because you don't know what to do, or don't know what 10% means, you're screwing the team. If you have all those bases covered, you shouldn't have any problems.
For PvP where everyone and their dog is using the STF shields with high plasma resists, then plasma weapons are a bad choice - but for PvE vs the Borg, unless the NPC's have a specific resist against plasma damage, then I can't see a problem. I recently outfitted my fed sci officer with a full set of purple MK XI plasma DHCs and Turrets + blue MK XI plasma tac consoles for his advanced escort from the exchange for chump change, and although the proc is underwhelming, I can still burn things down very quickly.
Personally I like the disruptor proc the best as it acts as a team damage multiplier, but the most useful thing to bring for STFs is IMHO attack pattern beta, and a full matching set of weapons + tac consoles.
probably tetryon are not suited best for stfs since some of the bigger borg targets don't even have shields and those who have do not regenerate them. other than that pretty much any energy weapon type, including plasma (borg do not actually have a plasma resistance, don't know who ever came up with that BS) are good.
torpedos i'm convinced that photons are best, because of the high firerate and the 100% proc. thats 1000 dmg free each time.
more important than weapons are tactics and teamplay anyway.
can you give me some advice on what the best weapons (I.E - Torpedo Launchers and Phaser Banks), are to fight against the Borg in PVE Cured and Infected Space??
I'm really confused on which are really best to use
Absolute best would be Anti Proton or Disruptor for weapons and quantum for torps in a standard build. That said the actually difference is so small its not even worth worrying about (less than a percent DPS increase overall I would thinks). So just stick to a single type so you can match the consoles and your good to go.
There are several build threads in the Federation Shipyards as well, or the PvP forum if you are looking for detailed advice.