Since the sticky for mods hasn't been updated in over 2 years and I'm currently sorting through my games and testing patches and mods I though I drop a few comments when I'm currently at deus ex.

I like to keep it as vanilla as possible.

1. Kenties Launcher .
Extract to your Deus Ex/System folder.

2.Human Renovation.
Bug fixes. Extract the files in the system folder to Deus Ex/System.

3. Kentie's Direct3D 10 renderer.
Copy the files from the Deus Ex folder to you Deus Ex/System folder.

4. OTP UI Fix.
Copy to your Deus Ex/System folder. That one took me a long while to discover. If you don't install the UI Fix but you already have Kentie's launcher and the D3D 10 renderer you will get a startup error.

5. Biomod.
Copy the files to your general Deus Ex folder. I prefere Biomod over Shifter due to Shifters skill point reward system which just doesn't feel right.

6. GMDX.
Graphic Overhaul that includes HDTP and New Vision. Just follow the setup. Didn't play too much with GMDX - but what little I've seen is pretty promising. Especially the options to edit the color of buttons, text etc. is really nice to make the HUD and inventory look matrix-ish with green and black. Make sure you use the GMDX.exe to play and enable GMDX, HDTP and New Vision as Data Directories in the launcher.