dosfsck - yes, thanks. It turns out that while that didn't fix the whole mess it did happen to recover the files that weren't backed up elsewhere. Yay
Having retrieved the data I then put the stick back into service by:
1) whacked the MBR (on purpose this time) using dd
2) fdisk the stick to a single FAT32 partition
3) mkdosfs the partition to a usable filesystem
4) install TC / MC 3.6 and 3.7rc1
5) set the whole mess up with grub4dos (native) instead of grub-0.97-splash. I like g4d but that bit where it searches for the boot files can make it tricky if you're booting from a usb stick and the internal HD has an older version of TC on it. I worked around that by having it search for a marker file that is unique to the stick instead.
Works like a charm. I'm thinking about one- or two-pass full disk test to verify the media just to rule out any hardwaare related failure on the stick. I suppose SpinRite would pretty much shoot the lifetime of the flash memory.