Was on a modern (Intel i5, etc.) 64-bit Windows 7 desktop and I used the following:
SS2 Tool -- Patches/fixes things up so the game is 'mod-ready', run it first after install. Here:
http://www.systemshock.org/index.php?topic=4141.0
SS2 Mod Manager -- Install this secondly. Basically open a mod (zip/rar) like the ones below with it and then click a few buttons to install and 'activate' them.
http://www.systemshock.org/index.php/topic,527.0.html
SHTUP -- Big texture pack.
http://www.systemshock.org/index.php?topic=22.0
Straylight ADaoB -- Fixes bugs and such.
http://www.systemshock.org/index.php?topic=25.0
DeepFriedBeer Sound Upgrade -- For weapons only, not music or voices.
http://www.systemshock.org/index.php?topic=27.0
Tacticool Weapon Replacements -- Better weapon textures/models, which is nice since you see them so closely and constantly! I believe I ignored incompatibility issues and they still worked fine.
http://www.systemshock.org/index.php?topic=691.0
You could also try the 'SHMUP' music mod, don't know why I didn't use it. And there's the 'Rebirth' mod, but I think I avoided due to potentially serious compatibility issues.
As I recall, supposedly it's safer to not install the game to either 'Program Files' folders. Instead, just make a 'SS2' folder in C: and install there. You may have to manually copy things from CD, which I didn't have to do but heard it's a common inconvenience.