Just pick the weapons you like and change the name. The Dominion's Polaron Beam weapons sound like a great possibility, they cut right through shields, and it took months to find a way around that weakness. Just call it an anti-proton-whatever weapon. Being the narrator, you have to still think that the object of the game it not to make your PC's lives living hells, it's to challenge them and have fun.
Usually you may want them to run into a ship slightly more powerful than theirs, it gives them pause from shooting first or even second. Like in Nemisis, when that Scimitar decloaked, and they found out it was armed to the teeth. That's one of those suspenseful moments you can create. If your aliens don't have cloaks, it can come out from behind a asteroid, planet, or moon. Or come out of a nebula, any dramatic entrance will do.
"Retreat?! Hell, we just got here!", annonymous American Marine, WWI
"Gravity is a harsh mistress....", The Tick