If Doom 2 had another boss

Satanic Mecha-Hitler, and a horde of Nazi soldiers.

a ninja

a clown

EDIT: a clown clone
EDIT2: of Michael Clooney.

RyRy13 said:

http://www.youtube.com/watch?v=dH-LUM-hAtY

Should have been this.

* http://www.youtube.com/watch?v=eNPD1hOOeps

Or : Cyberdemon , Spider mastermind , two barrons of hell. In one big room with a pilar as defence. (no infighting)

Fighting this thing would have been awesome.

a stegosaurus that shoots rockets from its tail

I'm down for the Cyber-Mastermind myself. Perhaps with Arachnotron turrets on all sides, too, so that it can shoot plasma in 8 directions at once. Ooh, and have the Cyberdemon part able to rotate independently of the body, so that it can fire rockets and its chaingun in two different directions. Maybe not useful for singleplayer, but it would make coop battles even more interesting.