I plan to add links to source ports like Chocolate Doom, EDuke32 or DXX-Rebirth in the OP. Post them if you know them and (preferably) used them (so we know that they aren't shit).
Well in that case …
Rise of The Triad:
WinRoTT.
Rise of The Triad on Windows. Works well and there is an OpenGL version in development for those who like that sort of thing.
Marathon serie:
Aleph One.
It comes with the three games for free; try them, they are cool! Not specifically a PC game in the Windows sense, but Marathon 2 was released for Windows at some point, so …
Wolfenstein 3D:
ECWolf.
First Wolf3D source port I found that wasn't a pain to use. Maybe not the most accurate, but then Wolf3D isn't a game where that matters much, unlike Doom and its hoard of user content.
Outrun:
CannonBall.
Not a PC game but worth a mention anyway: it's a new engine for the old Sega arcade classic Outrun. Features various enhancements, the ability to mix tracks from Japanese and US versions, play all tracks in one big game, fixes the music bug that affected the game for two decades, etc. Requires the original ROMs (MAME ROMs work). Not vanilla at all but that isn't its purpose, so if you want that you better stick with MAME.
Dungeon Master & Chaos Strikes Back:
CSBwin
Not really a source port, since the source was never officially released, but it's a port written from reverse-engineering, and apparently quite faithful. It plays Dungeon Master and its stand-alone expansion Chaos Strike Back just like they played on the Atari, with some small addition like remappable keyboard shortcuts. Configuration isn't user-friendly though as you need to manually edit the config file, but once set you won't need to touch it again.
WARNING! Chaos Strikes Back is rated "Not For Bitches".
The download page I linked stays within the general theme of annoyance of setting the thing up, but the latest executable as of writing seems to be the 12.8 release, dated 2013-11-02. There is also a
template config file you might need. The games are on
this page and already contain an older CBSWin executable that you can easily replace with the newer one.
Dune II:
Dune Dynasty
A modern port of Dune II based on reverse-engineering of the original. Adds a few enhancements like a bigger viewport, multiple unit selections, or a construction bar on the right side—pretty much what you'd expect to see in the C&C serie. It might make the game too easy because of this, but it certainly makes it more enjoyable for those used to modern features—I always found it painful to select each unit one by one before sending them to assault the enemy base. There is an option for a more brutal AI, probably to balance this. It displays briefings and cutscenes as expected, so it really plays like a modern update of Dune II. Not vanilla since it isn't the purpose, but stays faithful to the original.
Ultima VII:
Exult
The classic!
X-COM: UFO Defense:
OpenXcom
Not a source port but a clone that tries to replicate the original, fixing bugs and adding a few optionnal features. Not 100% vanilla but can get pretty close if you set it up that way.
I already wrote about Chocolate Doom earlier, and it might go beyond the scope of this thread, but I might as well mention
Crispy Doom. Crispy Doom (the ill-named) is a fork of Chocolate Doom that offers a few enhancements while staying compatible with Vanilla Doom. The most visible feature is that the resolution has been doubled compared to the original, so you can enjoy Doom in 640x400 (many official ports apparently do this, including the old MacDoom and Doom95), but it also raises the limits so larger maps that would crash under Vanilla and Chocolate Doom will play fine in Crispy Doom—one of the best examples of this would be the No Rest For The Living episode (NERVE.WAD) that comes with Doom 3 BFG Edition and is actually a great set of levels for Doom II. It includes some definitely non-Vanilla features, like jump—I consider this a cheat but some new Doom maps are designed with that feature in mind—, but these are disabled by default. If you are concerned about this, you can have it play just like Chocolate Doom but with higher limits for larger maps—it's even possible to change the resolution back to 320x200 if you are an absolute purist, although the origins of that limit are purely technical. Development is strongly tied to Chocolate Doom, so any new version or patch will see an update of Crispy Doom. Development focuses mainly on Doom, and though it is possible to play Heretic, Hexen, and Strife, in Crispy Doom, they are likely buggy.
Else for those who want more bells and whistles, I recommend
ZDoom as the port with enhancements. It has many screen size and aspect ratio options, pretty much removes all limits so it will play everything Doom related you throw at it, and fixes all engine bugs. It is apparently smart about it and will reactivate bugs needed for some maps of the classic WADs so they can play properly. It of course can play all modern WADs that are based on it, like Chex Quest 3, that won't play at all on Vanilla Doom. From my own experience, it deviates too much from the look and feel of classic Doom—Romero said that one of the great things about the Doom engine is that it is naturally scary with the way it adds darkness to the map, so he didn't have to bother too much about that and just design his maps and the engine would take care of the scary atmosphere for him—but I know many aren't bothered by it. If anything, it kinda manages to be very modern while staying true to its classic foundation, so there's that.
So basically I'd say go for Chocolate/Crispy Doom depending on how much of a purist you are (Chocolate Doom is preferable at this point for Heretic, Hexen, and Strife), and ZDoom if you do not care for all this stuff and want the new shit. I'd stay away from stuff like Doomsday as the dynamic lighting effects regularly screws up the look and feel of classic Doom, but that's just me.