Being the big Q1 fan that I am.. it's only natural that I pick Doom2. Best enemies in a game by far.. Arachnatron taught me how to circle strafe, and Mancubus was just cool. Other favorites are the annoying Arch Vile and the awesome Chaingunner zombie (for obvious reasons).
Being a Q1 fan, it's also natural that I pick Wolf3d as a close second. Nazis are always fun to blow away.. Hans Grosse is just badass, wishing everyone a good day before turning them into swiss cheese. Hitler is just the icing on the cake.
Quake comes in 3rd.. the Fiend royally scared the bigeezus out of me when it first leaped across the room and smacked right into my face. Vores with the overly annoying purple spiked balls of doom, Shambler with the insta-hit lightning, and the lowly Zombie with the awesome description in the manual.. the Enforcer was a personal favorite tho, and is now forever immortalized in Gen thanks to Tab's awesome model and skin work.
Doom is 4th. Nice demonic enemies that fit the atmosphere of the game, but I feel they're not up to snuff when compared to the top 3. Spectres in dark rooms are hella fun tho.
Quake 2 comes in last. I'm not a fan of the bio-mechanical theme the Strogg have going.. but there are two notable exception. The Tank/Tank Commander are badass.. slow moving, heavily armed and armored machines of death. The unsuited Makron is also neat.. mostly because he reminds me somewhat of Shockwave from the Transformers. Makron has the railgun head, giving him a dull and lifeless feel.. much like Shockwave's single yellow 'eye'. The rest of the lineup is pretty lame and boring.