Let me add my 0.02$ here -- the reason of Out of Theme items in DoomRL.
As you all know, only uniques appear out of theme, and that's really how I would like it to stay. The general out of theme way that happened is just because it's hard to come up with a lot of uniques that are in theme with DoomRL. That in mind however, there are a couple uniques that have a strong reasoning behind them:
Spear of Longinus/Angel of Death (and Angelic Armor as a companion) -- this is an obvious reference to Wolfenstein/Spear of Destiny. I allowed myself this inclusion on the same principle that there are Wolfenstein levels in Doom 2.
Railgun, Blaster, other Quake related items -- obvioulsly also from Id.
Dragonslayer, Butcher's Cleaver -- a homage to other Chaosforge roguelikes.
Grammaton Cleric Beretta, Malek's Armor -- a homage to Malek, who while now being inactive, played a vital role in the beginnings of Chaosforge Forums.
That leaves Trigun and Anti-Freak Jackal. The references aren't that strong, and I desperately needed some new unique pistols.
The rest of the uniques is more or less in-theme.