I am building a new gaming system, and I want to install Windows, Steam (and therefore all my Steam games), as well as all my non-Steam games on a SSD and place the rest on a HDD. However, this seems like it would require doing something tricky with my Program Files directory. If I install Windows to the SSD, how can I install all the other stuff that goes under Program Files to the HDD? Further, Steam installs under Program Files, so how would I reconcile that? I know you can fool around with ProgramFilesDir in the registry, but Microsoft seems to imply this isn't safe. Do you just have to completely abandon the Program Files architecture, and when it comes time to install a new program, just change the destination to some random directory on the HDD?
You can install the Steam program and your games on any of your drives.
It's only that C:\Program Files is the 'default' install location. Just choose another of your drives.
Installing Steam (YouTube video) http://www.youtube.com/watch?v=w0hJrn5ZgMM
How large is your boot SSD? You might be better off using the SSD for your OS and games if it's large enough.
Picking up on what LePhuronn said . . . the ideal situation is, say, a 120GB SSD "C" drive with any larger mechanical HD as "D". The OS and all active games (apps) go on the SSD. Photos, music, etc. and related apps go on "D". As/if you need to manage the use of the SSD, move or delete old games.