I usually just use Skulltag to play Doom, Final Doom, Doom II, Hexen, and Heretic. Never tried Strife. My main reasons for using it is for the better control options. I'm not use to holding a button to strafe. Skulltag also allows aiming up and down. However I have no luck finding mods that offer better control options for Wolfenstein 3D or Wolfenstein 3D: Spear of Destiny.
Also, if anyone knows any mods like EDuke32 for Shadow Warrior and/or Blood please let me know.
For Shadow Warrior, try Proasm's SWP. http://www.proasm.com
Anyway, you mentioned that you use Skulltag but seriously, check out the Doomsday engine. It has modern control options, has vertical aiming, you can even turn on jumping if you want to. The engine has a lot of different lighting options too, making torches and other objects into lighting sources, and playing at high resolution makes an immediate impact. Also, you get the option to install full 3D models, particle effects, and other addons.