Doom + Doom 2 + Master Levels +Final Doom
I know little more of protocols than that games like Doom, Doom ][, Heretic, Warcraft II, etc., use IPX, which MS decided to no longer allow under Vista and W7. I already own the games on CD, but once my older machines die, I might as well use the CDs for coasters. The wife and kids and I are not big fans of any of those in single player mode.
If GOG were to figure out some way for those to communicate over TCP/IP, or created some program to fake the protocol, I'd be all over it!
I'd recommend ZDaemon or Skulltag. I've only used ZDaemon of those, but they should have basically the same features - anyway, they're multiplayer server browsers that support all the Doom engine games, by running them through a slightly modified versio of the ZDoom port using TCP/IP.
Quake 1 has nQuake, which uses the QuakeWorld netcode with the TCP/IP protocol (making it 100% compatible with all the classic QuakeWorld clients and servers), it has some graphics "enhancements" that are slightly hard to turn off, but with a couple of lines into the console you can get the game to look almost exactly like the classic software rendered quake - even though it's running through OpenGL.