Doom, Doom 2, Hexen, Heretic, Strife
Chocolate Doom is a source port for Doom and other games based on the same engine. Other ports exist but mainly aim to add new features while Chocolate Doom tries to faithfully reproduce the way Vanilla Doom originally played back in the '90s, including bugs and other limitations. It lacks the bells and whistles of other ports but the games will look and feel the way they were designed to while natively running on modern systems without the need for DOSBox. While it may be tempting to use another port with more features some of these may change the gameplay in the subtle ways, for instance dynamic lighting systems might remove a difference in lighting that can be a clue to a secret area. Chocolate Doom can also play old maps and mods created for Vanilla Doom that won't run in more modern ports.
Edit: While on the subject this page may be useful if you want to check the version for the various WAD files and ensure you have the latest ones:
http://doomwiki.org/wiki/IWAD If you do not have the latest version you can always track patches for them on the net but may need to use DOSBox to apply them.
It is worth nothing that for the best experience you should use the original WADs and not those that come from the BFG Edition of Doom 3 as these contains some silly changes (censorship of the secret Wolfenstein levels, Nightmare! difficulty toned down, red cross logo of stimpacks changed to a pill) and potentially some bugs. Spare yourself the trouble and use the files from the regular releases of Doom.
Final Doom is interesting. It consists of two WADs, being TNT: Evilution and Plutonia Experiment and both have bugs — minor for Plutonia and game-breaking for Evilution. Evilution is infamous for having the yellow key card being flagged as multiplayer-only in map31, making it unable to be collected in single-player and thus preventing the completion of the level — it's possible to do it with glitches but you'll have to admit it's less than ideal; the popular fix is to use
a PWAD released by TeamTNT to patch the issue. The weird thing is that while id Software never officially released a patch for the issue, some versions of their '96 anthology contain a WAD with the bug fixed as well as some minor changes. That version also features a fixed Plutonia WAD where the multiplayer spawns on two maps are correctly activated this time. The trick is that only a handful of these anthologies have the fixed WADs and the rest have the original ones, and since all packaging are identical it is a bit of a mystery why this happened. Even the Final Doom version being currently sold on Steam has the original unfixed WADs, so it's like someone at id fixed that stuff without most people knowing, it made its way on some anthology CDs, and then it went unnoticed. So in case you got your Final Doom WADs from Steam, be aware that you'll be stuck in Evilution unless you apply the fix linked earlier, but I guess you can live with the 2 maps in Plutonia being unavailable for multiplayer. Of course you can always track the updated WADs on the Seven Seas if you wish, but their scarce status might break compatibility with demos and the likes if that is important to you — it doesn't for me.
Lastly the first, and most commonly distributed, version of Final Doom has 2 bugs tied to the executable. One is that the game will crash if left on the title screen too long. Reason for that one is simple: Final Doom is based on the Ultimate Doom source, and UD has 4 demos while FD only 3; FD will play its 3 demos and crash when it expects to find the 4th. The second bug affects teleportation: the Z coordinate isn't checked, meaning the player may spawn on the ground just as he may spawn in mid-air. The second release of Final Doom fixes both bugs, but again due to its rarity it may break external stuff. Chocolate Doom can emulate the game version you want but due to the fact the first version is most common, it will by default load the 2 Final Doom WADs as that one. This can easily be switched though by using the "-gameversion final2" command-line argument.
