FAT32 sucks!

I'm doing my monthly offsite backups and am seriously frustrated by the limitations of the FAT32 file system again. FAT32 is something of a de facto standard since most external hard drives and USB flash storage devices come pre-formatted with FAT32. However FAT32 carries with it the limitation that the size of an individual file may not grow beyond 4 GB. Many backup programs don't handle this limitation gracefully since this requires the backup program create multiple output files.

So what are my options for getting around this limitation? I'm currently using external drives with 2 partitions equally split between FAT32 so the Windows machines can write to it and HFS so our Macs won't be limited by the arbitrarily small maximum file size. Another option is formatting the entire drive with NTFS and using MacFUSE/NTFS-3g to allow the Macs to read and write to the NTFS partition. I like this approach better as it doesn't force me to correctly predict how much space I'll need for each type of machine.

Ultimately I think I'd prefer to use drivers to allow me to mount, read, and write to Linux EXT file systems but this requires more investigation. This is mainly because I really hate the thought of trusting my Mac data to NTFS.