AFADoomer.com: AFADoomer's Wolf3D and SOD conversions in Doom 2 using Simbey's program.
Chucktropolis: Online Residence Of Charles Jacobi.
Doom Legends: Deimwolf, The Ultimate Chex Quest, and The Epidermis Emporium. Carefully look for Blake Stone, Commander Keen, and Wolfenstein 3D skins for Doom 2 here and here. There's also the chicken from Heretic.
Doom Wad Station: Comprehensive DOOM site with a Wolf3D section. Hosted by Bob Larkin.
Doom X - Home of the Flesh Wizards and Gangsta Grosse: What it says. Has a number of interesting videos. Hosted by Melvinflynt.
Doomworld/idgames: ID games archives database.
DOSBox: DOS Emulator page.
GZDoom Wads: GZDoom Wads, hosted by DoomWadStation and dedicated to the Graf Zahl's fabulous port Emulator page.
Hell On Earth Sound: Doom Music, including the secret level 31 of Doom2.
Miasmata: James Redmond's site
NewDoom.com: Dedicated to the fans and community of id Software's Doom games.
OldDoom.com Archives: Patches, manuals, wads, editing, files, and everything else you need to know about Ultimate Doom and Doom 2
Paul's Doom Page: Good selection of wads and music. Hosted by Paul Corfiatis.
PlanetDoom: Doom Movies, Maps, News, Resurrection of Evil, Cheats.
Realm 667 dot com: The Ultimate Torment 'N' Torture, Armory of Guns, Beastiary of Enemies, Prop Stop, Special Effects Shoppe, Texture Stock, and more links.
Simbey's Wolf3D To Doom Converter: What it says.
WolfenDOOM: and Laz's Wolfenstein 3D (Macintosh) Page: WolfenDOOM mods info and screenshots. Hosted by Laz Rojas. I couldn't have made this page without Laz Rojas!
ZDOOM.org: Enhanced DOOM port for Windows. With compiled and source downloads, development news, tutorials for the new features and a discussion forum.

MS/BL.