A pulse transformer (salvage it from a LAN card) or opto-coupler would be advisable where the power source isn't common. For applications like a wavetable daughterboard, I see no reason for anything special unless you have problematic impedances on either input or output.

Thanks for the anwer gdjacobs. The FTDI board gets power from the USB port of another computer that got it's own PSU. Both computers runs from the same grounded AC circiut. Would modifying the FTDI board to get 5V power from the computer that contains the sound card instead be an idea?

I'd probably do that or add some isolation. It's really more to prevent Bad Things resulting from Oh Shit moments down the road if the FTDI adapter is used another way without further modification. I don't believe you're going to see much difference in ground potential between the two machines if they're sharing the same ground point. You could probably strap a note to it reminding you that the adapter isn't isolated if you just want to mess around some more without doing further work.

I now tried using the "Roland Serial MIDI Driver" instead of "Hairless MIDI<->Serial" utility and "loopMIDI" combo on an XP machine to get less overhead. It works but when using the FSMP I have to accept the settings once again whenever I start a new game or else I got no incoming MIDI signals to FSMP. I think this is an issue with the Roland driver.

I also experimented a bit using Ubuntu with promising results.

I did some more experiments with Xubuntu as I mentioned here. I used the "serial MIDI kernel driver" to get the MIDI commands fed into ALSA and the "setserial" utility to change the serial speed to 31250 bps. This guide helped me getting the permissions for the serial port right. For compiling and installing Munt I used gdjacobs excellent guide, just skipped ARM specific part. I noticed one problem though, It doesn't seems like the FTDI adapter gets outgoing MIDI commands, but for my usage it doesn't matter.

I also noticed that you can get isolated FTDI adapters on ebay for about 5 GBP from China, perhaps they would be perfect for this application.