I remember when Wolf3D came out, we played it a lot on a friend's 386 (I didn't have a computer at that time). I was hooked. Then, shortly after we bought our first PC, Doom came out and I got the 2-disk shareware version from a friend at school... even though performance was not great on my 486SX with 4MB I spent lots of hours on it, and it was the game that got me into the whole hardware upgrade thing 😁
But my favorite of the non-3D shooters has to be Dark Forces, diverse environments, cool weapons & enemies, Darth Vader and a compelling story with cutscenes, that game had it all!
However I cannot say that I didn't enjoy the first 3D shooters... loved Quake I & II, Unreal, Half-Life, Jedi Knight and so on. I think that the fact that those were actually good games got augmented by the awe I got from early 3D accelerators (Voodoo2 in my case).
The last 3D shooter I fully enjoyed was probably Return to Castle Wolfenstein. That one kind of marked the end of an era to me, as most of my friends either got into console gaming or just stopped playing altogether, and I turned into other types of games like RPGs and 3D person.
I really liked Doom 3 though, I'm one of the few who prefers slow paced 3D gaming with scares rather than running all the time while shooting. That's why I've been reluctant to play the new Doom, in fact I played the original one quite slowly and had fun so it kind of grates me when people say Doom is all about "never stop moving and shooting".