I've been using this recently and, because it doesn't ever modify the file system structures, you don't have to worry about unmounting the volume cleanly.

It can write to files, but it can't create or resize them. For that (and more), you want FatFs, the full featured version: http://elm-chan.org/fsw/ff/00index_e.html

elm-chan has also written an AVR bootloader that can update the flash from, for example, an SDCard. It uses this Petit FAT File System Module and requires a 4K bootloader section (so mostly of use on the ATMega1284).