The one stop shop for a Vanilla+ System Shock 2 Playthrough. There are plenty of other good graphical/sound mods out there, but these are the basics.
READ THE TOP FORUM POSTS FOR FAQS AND HELP, THEY'RE FILLED WITH THE WISDOM OF THOSE WHO MADE THESE MIRACLES
Guide has been *slightly* updated for clarity and some other stuff
1 - System Shock 2 Tool, you should ALWAYS want to have this no matter what:
https://www.systemshock.org/index.php?topic=4141.0
2 - You should want the Blue Mod Manager installed during the wizard installing SS2 Tool, you can then plug the following zips right into it using the install mod archive feature.
2 - The Community Patch (SCP), grab the RealSG addon while you're here:
https://www.systemshock.org/index.php?topic=7116.0
3 - The SHTUP Texture Replacer:
https://www.systemshock.org/index.php?topic=22 (main site
http://www.shtupmod.net/)
4 - The Four Hundred Terrain Replacer:
https://www.systemshock.org/index.php?topic=4240.0 (main site
http://gaarabis.free.fr/index.php?catid=2#SHK2_400_jump, though this version is older)
5 - The Load Order might take care of itself, but it should look like from top to bottom with each having an Active status:
Four Hundred v20U
SHTUP-ND-Beta1
RealSG_1.05
SCP_beta4
Your computer will be HAUNTED if you put a single skill point in repair.