Second Dark Forces (AKA Jedi Knight) has an engine that post-dates Quake.
Anyways I thought I'd share my thoughts about all the games in the list:
Wolfenstein 3D/SoD: Well that's what I'm on these forums for, primarily! These games are so old but just like others, I always find myself coming back to them. Definitely classics.
Lost Episodes: I am SO glad to know these weren't made by ID not only because that means I can list them separately (for reason of different developers), but also if ID released these I'd be saying WTF?!. Seriously, these should NEVER have been commercial at all.
Blake Stone series: Played it, they are okay, but despite the fact that they add elements Wolfenstein didn't have, there are so many key elements that made Wolfenstein work so well - the graphics, the level designs, the atmosphere, the story, the setting, and just the overall feel that just aren't replicated here so for me this game fell into mediocrity. It is probably the best Wolfenstein engine game other than the real thing, though. But very, very distant from Wolfenstein/SoD.
Other Wolf engine games: Haven't played them, though I know none get very good reviews.
Classic DooM series: Obviously another favorite of mine. It is THE classic among all oldschool FPS games, the biggest staple in the entire oldschool FPS community, and saying it's classic is an understatement. Nuff said.
Heretic: DooM knockoff, but actually like it, for the medieval atmosphere and the level design. There are extras for it too, but overall I think it's under-appreciated, and under-modded. Seems like most just go to DooM instead.
Hexen: A lot of people like this, but too much in the way of frustrating puzzle like gameplay for me. Plus even fewer extras than Heretic.
Strife: Last of the DooM engine games, and again some find appeal in it, this time due to some merging of RPG elements into the mix, but it didn't really strike me as much. And there's even few extras than Hexen, if that's even possible.
RoTT: Shameful miss from the list, so much so that I'll include it here. It's definitely a game to have a niche for, with multiple reasons behind that, though I feel it gets boring when played for too long at once.
Dark Forces/Outlaws: Haven't played them, though I'm interested particularly in if Outlaws is something I should go grab (Star Wars frankly doesn't tempt me as much as it should).
Descent games: Completely different from anything else in the list because there's no gravity and you are flying. Very cool concept IMO, and I like it generally, though the games do have their flaws, including rather buggy engines full of hacks and very convoluted game coding. Still, I feel they never got quite popular enough.
Duke Nukem 3D: I honestly don't understand why it isn't almost as popular as DooM. Sure it's one of the more popular games in the list but as long as you can take some language, I don't see anything wrong with this game at all. It takes DooM at its heart and builds upon it in multiple ways (and ironically, it's called the Build engine)! Such great humor and jokes, if you can handle them and know they're just jokes and it's just a game. A definite top five from the list for me.
Shadow Warrior: Haven't played this for a very, very long time but remember enjoying it. Who cares if it makes fun of Asians? It's just a game! Yet somehow popularity and overall ratings pale in comparison to Duke.
Blood: Scary horror atmosphere and good, tough levels make this another favorite of mine, and another under-popular one as well. I wish it had an engine such as EDuke for it, but sadly it doesn't. Once again seems under-popular, though if you like the game, I've heard there's one really good and really large mod for it called 'Death Wish'. It's on ModDB somewhere; just search.
Other build engine games: Didn't even know they were Build engine games except Redneck Rampage, which I forgot to include but isn't it just a cheap knockoff anyways? Still, I would have included it if I had thought of it.
To review an earlier post, I made four picks: Wolfenstein/SoD, DooM series, Duke, and Blood. And like I said, a mod can feel free to add games I didn't include that use a pre-Quake engine if desired.
(Though please enable vote canceling if such is done as well so people who wanted to vote for them can add in their votes)