First, connect all the teleporters to the mainframe. Then for 5000 you can put your gun in Pack-a-Punch and it will be given back to you upgraded. Basically, it has weird tribals on it, hits harder/goes through surfaces and bodies better, fires faster, etc
actually the most useful part, generally speaking, is the upgraded ammo. you get double the clip size and double the reserve basically. While it doesn't apply to say the colt which turns into a grenade launcher, the extra clips come in handy when you get to later rounds and everyone runs out of ammo.