I don't have much time at the moment to work on the MEGA65, but we have been able to do some planning on which ports we expect to support.
The following is what we have made electrical provision for. Note that this is different from what may be on the actual main boards, due to space and/or cost issues, but it is the set of ports that we should be able to support, all with real 5V signals.
1. Stereo SID sockets
2. Stereo RCA audio output
3. VGA video output
4. 100mbit ethernet
5. 34-pin floppy drive interface (720k, 1.44MB and hopefully 2.88MB floppy drives, as well as 5.25" PC floppy drives although we aren't putting special effort into this).
6. C64 and C65 keyboard
7. joysticks (with full paddle support)
8. Expansion/cartridge port (initially only relatively simple ROM cartridges, but we have all signals plumbed, including DMA)
9. IEC serial for 1541 and other Commodore floppy drives
10. Extra SD card socket (in addition to the microSD socket on the FPGA board)
11. Cassette port
12. MIDI interface
13. Composite video (although it will initially be 100% compatible with the C65's composite video port -- i.e., it won't work ;) -- we are just making provision for implementing it later on.
14. DVI/HDMI video (this also won't work initially)
The main omissions compared to a real C64 or C65 is the user port, which shouldn't be any need with all the IO options on the MEGA65.
When I have more time I'll explain how we are connecting all this stuff using just 40 I/O lines on the FPGA. Perhaps after we have had a chance to see if our way of implementing it actually works ;)