I put in a smallish but fast (500GB) VelociRaptor HDD (E:) for installing programs that are bulky but that I use rarely and are not speed-critical. Created two directories, Program Files and Program Files (x86). Anything occasional goes there - neither Windows or the apps seem to care and it keeps the boot SDD (C:\) clearer.
All my data files (Documents, Pictures, etc.) data goes to 2 separate mirrored HDDs - [D: for Data]
(You can also use a second SDD for additional app installs if you like - I did that on my son's machine, but he's a gamer....)
Mac
:-)
PS: Some older apps are hardcoded to go into C:\Program Files and won't install anywhere else.