- DOOM, DOOM 2, ...: For the best "retro-feeling" I recommend Chocolate Doom. If your distro doesn't package it, just grab the source and build it yourself, it's not hard. Youngsters may not like it because it's designed to give you an "accurate" 1993 experience (pixels!), but that's how it's meant to be played so deal with it.
- Quake, ...: The only thing I can recommend is the DarkPlaces engine. Don't get me wrong, it's an awesome effort and it does indeed look a lot better than the original. But my vintage 2009 graphics card actually has trouble keeping up which is a little sad for what is ostensibly a 1996 game. Alas, every other source port I tried didn't actually work, so... Also surprisingly easy to build, just grab the source and hit make. Just be prepared to wait a little longer than for the Chocolate Doom build.
- Quake 2, ...: Even fewer choices for Quake 2, but luckily Yamagi Quake 2 is excellent and they didn't overdo it with the graphical polish. I can play this at full speed with all the options turned up and it looks more or less like it should. Once again a pretty easy build, just grab the source and boom there it is. One minor quibble: They don't have a command line flag to configure the base path, so if you don't want to throw the executable into your data partition you'll have to change two lines in the Makefile.
There you have it, the stuff I've been playing with over the last two weeks or so. Good clean retro fragging, who can resist? I may update this post with more details if there's interest, so leave a comment if you prefer another engine that I missed or if you can't get the above to work for you.