All the default folders of the user:

Documents

Downloads

Music

Pictures

Videos

My Virtualbox build directory

.thunderbird

a note pad directory

an "isolibrary" directory I maintained

Most software like View Your Mind, Calibre and others gave the option to choose where to save a file which normally went in one of the above.

google I didn't concern myself with because they hold config info and once the user signs in then chrome takes care of itself usually.  Config files I didn't concern myself with unless, like Thunderbird, had some specific databases I wanted preserved.  Most of the rest was just flare and tweeks which, tbh, I didn't mind changing up at the time.

Main thing to remember is KISS.  This is a simple way to have the normal drop points of data redirected to the larger drive.  If you want a true separation per user then you might consider an ldap or other similar solution which maintain user data and options on a specific database and no matter where they log in then their information and choices are available.  Mine was just a share on how I did things in a similar situation with drives and is practicable for maybe up to 6 or so users; because of the manual nature of linking.