Ryleh, I hope I'm not missing something thats in the readme, but a couple of questions that are suggestions for the future if there isn't a method to do these:
1) How do you switch disks for multiple disk image games?
2) Virtual Keyboard - are there any more keys than the 1-4 used by pressing select and U/D/L/R? If not, the only one I really miss is I believe 5 (tagged to run?) that I think was available on an earlier version of fMSX by hitting select w/ the virtual keyboard (keys changed).
If these aren't availble right now, just consider them possibles for the future, these are very minor thing,s you've done great work!