I think, the weapons should look as organic as possible, such as the weapons from Prey
http://www.prey.com.
The weapons there are half organic half metallic, it is a very cool mix, and the noxons would match the species (i think

).
Also the weapons can be integrated fully into the ships or the persons, as some noxons might be fighter drones

(@beni: please correct me if this is not the case...)
Weapons may in this case be parts of animals that produce a toxic waste, or weapons might throw alien animals that explode on impact (maybe they are filled with gas or any other acid).
But most importantly, the weapons must look dirty, slimy and ugly. You (human) do not want to touch them, unless you have to...