Favorite: Daedalus. Icarus was one of my favorite enemies in Quake II and Daedalus basically made it even cooler. Plus, I always liked enemies with energy shields (harder to kill yes, but pretty neat to look at when you're blasting it with a Chaingun).
Least: It's a toss-up between Turrets and that hard-as-h**** boss in the Hangar (the flying one that can spawn Flyers). Turrets b/c they are just everywhere and are really annoying to take down (especially when you're out of Rail/Rocket ammo). The Flying boss b/c it was simply overwhelming to dodge his attacks, dodge the Flyers' attacks, and return fire at him, which is really annoying where there are hardly any cover.