Designing totally alien vessels

When you use the Starships book to design vessels for a totally new alien civilisation of your own creation and you want to include some alien weapons of your own designing does any one use a hard and fast rule for cost.

Specifically I have an idea for a race that uses subspace based weapons (the civilisation is from the far side of the Delta quadrant so to them the weapons aren't banned). They also use an anti-matter based beam weapon.

I generally want my players to experience a totally alien weapons system which will make their life hell (a la the Krenim from Voyager).

The rules presented are good for designing vessels for the most common fleets but they pretty much leave you to your own devices on creating a whole new breed of ship.

Any ideas?

WEll, I just use premade weapon systems in the Starships book, change the name, and possibly change the features to suit what I want. :)

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. :D
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.

I'd love to see some Andromedans from SFB.