It's somewhat common knowledge that Doom runs best under a source port, and that most WADs use one. What's your favorite?

I usually use ZDoom myself on my older computer, GZDoom or Zandronum on anything else.

You MUST try out the "Unloved" mapset for Doom 2!
You're gonna need a GL based source port for it though, I see you're already familiar with G/ZDoom.

Doom is very DOSBox friendly but I recommend Chocolate-Doom for closest to vanilla experience:
http://www.chocolate-doom.org/wiki/index.php/Chocolate_Doom

Yeah, Chocolate-Doom is my second after running the original engine in DOSBox.

If anyone's looking for other Doom-based mods or freeware games, there's Action Doom 2: Urban Brawl (free), Harmony (free), Mega Man 8-bit Deathmatch (free), and Batman Doom (requires Doom II+a patch for ZDoom-based ports).

There is also Doom Retro. It's an improved version of Chocolate Doom without multiplayer support.

It has some nice features (i.e. blue blood for Caco, moving liquids, etc.), but does only support a small number of mods.

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I use either GZDoom or Retro. (Sometimes Zandronum for multiplayer.)

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There are some other standalone games: The Adventures of Square (ZDoom/GZDoom) and Nocturen in Yellow (Gloome)

IIRC Gloome is a fork from GZdoom 1.8.1 engine with GPL code only, right? So, someone could use it for making his game and sell it.

Yes. That's the intention. I've wondered why it took so long for someone to start a project like it.

I stick to Doomsday Engine with the HD plugin and Abbspack.

Gzdoom if I'm feeling nostalgic and want sprites instead of quake-like polygon entities.

I usually use GZDoom for mods and ZDoom for vanilla gameplay.

I like Doomsday Engine due to better graphics, mouselook and having to aim at both the X and Y axis. Original Doom and most sourceports have auto-aim along the Y axis, which used to annoy me a bit even back in 1995. Doomsday just feels more like a true 3D shooter.
It can also run Hexen and Heretic.

Playing the original levels: DOSBox or Chocolate Doom for the "classic" experience.
Playing mods: ZDoom, it generally works well with most wads. (GZDoom if required.)
Online play: ZDaemon, but it's been a while, so I don't know if this still gets updated. I also hear Zandronum is pretty good.

And Doom Retro is a fairly recently addition to the list - it aims to recreate the look and feel of the original, with some minor enhancements.

Also, look here for (many) more options and info: DOOMWiki.

I prefer GZDoom because i like my Doom BRUTAL!!

https://www.youtube.com/watch?v=oSzYliSASKc

You don't know Doom when you haven't played Brutal Doom!

Works with GZDoom and Zandronum.

More like you don't know Doom when you've played Brutal Doom. It's so unfaithful and changes everything, you could say it's a different game altogether -- not at all Doom.

Yeah, also the author is a dickface, and has gotten himself banned on all major DOOM sites.