The Shredder gets my vote, I mean seriously that thing packs quite the punch, it's extremely versatile, and it's quite the spectacle. It's such a shame it creates so much lag on the N64, hopefully this is fixed on the HD Remaster. The Scorpion Launcher could easily be my second favorite, easily tops the Quad Rocket Launcher on Turok DH.
And obviously the Cerebral Bore is quite special and legendary.