We have two SNES controller ports which have been enhanced by assigning the unused two pins to the I2C bus; this will enable many accessories to be made for this port, including keyboards or other such custom interface devices.
The system supports four SNES controllers; the signals for all four are on the internal control header, suitable for whatever case design you have in mind.
The clock port does pretty much what the Amiga's clock port does, plus a debug serial line and I2C.