I've been doing some work with FreeNAS and I saw that it has shares for Linux, Mac, Windows.
Does this mean that in order to properly create a backup system that FAT32 is not an ideal option to share between all the operating systems?
FreeNAS (at least the one I've got remote access to) appears to be a Debian box running SAMBA, which means that it is doing Windows Filesharing in Linux. Depending on how you would back it up, I'd imagine the ideal filesystem would be ext4, as that is (at least in my case) the original filesystem - but this may prove difficult to work with under Windows and Mac
FAT32 would provide the most flexibility for cross-platform operation at the expense of loosing information about owners of the files - ie if you don't care about access controls, are not using files > 4 gigs and don't have very weird characters in filenames, FAT32 is a good solution for flexibility and portability.