For my own installation(s) spacecraft3 and multistage2 (with patched stage.dll) all get unzipped to the orbiter directory maintaining the file structure (so that modules wind up in the modules folder for example). Along with those go Orbiter sound, UGCO and DGIV.
This is my "baseline".
From that point I use the Jonesoft Mod Enabler. It created a MODS folder. All further mods find themselves there, each in there own folder. JSGME (when ran) allows the user to activate/deactivate mods as they wish. This can also very helpful for troubleshooting, as you can always "uninstall" everything to get back to the baseline to see what is causing a CTD.
I've got a few dedicated installations for a few projects; one for all things AMSO/Skylab 1873/1980, another for Wet Workshops, one for the Space1999 worlds, WO2001 and a beta to play around with.