FAT32 doesn't support symlinks, permissions,
ACLs and other advanced file features of
NTFS, you can't just copy system files from a Linux or Windows system partition to a
Anyways, you can create archive packages using applications that are able to preserve those features, and save those packages to your FAT32 partition.
For example, on Ubuntu Linux you can use
tar to create a backup, in a way similar to the following (I guess one can do something similar also on Windows):
# tar czvf /path/to/fat32/backup.tar.gz /
Still, you may run in problems, since
FAT32 file systems can't save files bigger than 4 GB, and often happen that a system backup needs to be bigger than that.
As a workaround for this problem, you can use a command similar to this to split the archive in chunks that can be saved on your FAT32 partition (see here for details):
# tar czvf - / | split --bytes=4000MB - backup.tar.gz.
Exists other tools, like
dar, that let you create backup archives and natively support automatically split on 4GB.
The 4GB limitation is really annoying, but if you use a system modern enough can be avoided formatting the partition in
exFAT is like
FAT32, but can save files bigger than 4GB, and any system newer than Windows Vista or Mac OS X 10.6 can read and write on it.
To use it with Ubuntu, you just need to install the packages
exfat-fuse that should be in universe repository.