Basically you have to either move the Tcl files of the modules you don't want out of your Tcl library or change their names to something else other than .tcl. I usually move them to a directory "notused" one level above the Tcl library.
Then move the www directories of the modules you're not using away from the www dir.
Somethings are annoying though. Some calls to functions from modules are tangled in several places. For example, I am not using the intranet module, but calls to im_user_is_employee (or something like that) are in "Your Workspace" for example.
This is where ACS4 is really a big improvement. There's true modularity.
