So many...
BFG 9000, Double-Barreled Shotgun, "Artifact" (DOOM/DOOM 3, DOOM 2, DOOM 64)
"Sticky" Explosive Charge (Red Faction)
Nuke, Minigun, Chronoscepter (Turok: Dinosaur Hunter)
Nuke, Razorwind, Cerebral Bore, Charged Dart Rifle (Turok 2: Seeds of Evil)
Blackhole Generator Gun (Turok 3: Shadow of Oblivion)
Rail Gun, Rocket Launcher (Quake II, Quake III Arena)
Redeemer, Shock Rifle, Flak Cannon (Unreal Tournament, UT2004, UTIII)
TAC Gun (Crysis)
Gravity Gun, Combine Pulse Rifle (Half-Life 2)
Portal Gun (Portal, Portal 2)
Plasma Cutter (Dead Space)
Spinfusor (Tribes)
X-Ray Gun (Perfect Dark)
Needler, Pistol, Rocket Launcher, Sticky Grenade (Halo)
Voodoo Doll (Blood)
V.S.S Vintorez (STALKER)
RPG, Srink Ray (Duke Nukem 3D)
Fatman (Fallout 3)
Sasha (Team Fortress 2)
And so many others, these above are just from the FPS genre (well except for Dead Space), I could keep going on and on for days about this, but I'll stop here.