Must say that I agree with kvasir and fishy_fiz here, and I would also like to add that both SFS and PFS can handle large harddisks with partitions over 2GB. This is somewhat possible with FFS also, but it has to be patched first and there are still some limitations.
Another thing is that SFS & PFS allows the use of long file names (up to 100 chars afair).
PS! I'm talking about the FFS version included with AmigaOS 3.1 and lower here, the version of FFS included with AmigaOS 3.5 & 3.9 do also support large harddisks, but I haven't tested this personally though.