As Bobby so correctly said; New Vision is indeed compatible with everything apart from Multiplayer, which causes mismatch errors.
For game play mods; Shifter, Human Renovation, Biomod and Patchv2.0 are not compatible as they all overwrite the same files. You kinda have to pick one and stick with it.
Also, HDTP isn't compatible with the current version of Patchv2.0 as it also has it's own deusex.u file.
Shifter, Human Renovation and BioMod have been made to work with HDTP using a coding method by Yuki (the Shifter dev).
New Vision, HDTP and Shifter do all work with Total Conversions such as TNM, ZODIAC and Redsun. I don't think Human Renovation and BioMod does work.
For convenience, I would use the new Deus Ex launcher: http://kentie.net/article/dxguide/index.htm
This is what mine looks like.