SUPER can handle mkv files just fine, and does everything the jodix converter can, too, it's just slightly more difficult to use, since you have to change several preferences for the converter to get the wanted result in iPod compatibility. If you have no idea on what specs to convert the mkv files into, take a look at the specs of the already converted videos, that might help. (Note for Vista: Run as admin. -_-)
If that sounds too long winded for you, you might take a look at the
Riverpast Crazi Video mkv to iPod converter or the
Ojosoft mkv to iPod converter, both looking a lot easier to handle, but I haven't tested them myself and can't give you guarantee.