Wiggy, you project-aholic...

On the SFC games, if it were me personally I'd just group them before or after the SNES games, since it's "kind of" a separate system, just like I'd separate NES and FC games if I had any of the latter.
But then, my case organization is kind of inconsistent - I put most console system games in alphabetical order, sub-organized(?) by series, so Super Empire Strikes Back and Super Return of the Jedi come right after Super Star Wars. But for Game Boy handhelds I organize them all in alphabetical order regardless of system, sub-organized by series, so SMB Deluxe, then SMA games in release order, and I have Super Mario Land 1, 2, Wario Land 1, 2, 3, 4. I also place games by what they are more commonly called, so I place SMW2 under "Y" as Yoshi's Island and SML3 under "W" as Wario Land. Sounds more complicated than it is, but my point is whatever works best for you is what you should do.