Yes, the FAT32 file system (which was most common for Windows 98 and Me users) is simple enough for there to exist drivers to let almost any operating system both read from and write to it, while many more advanced file systems are often pretty exclusive to one or very few platforms (UFS and HFS+ for macintosh, though there are programs to let Windows read and write to HFS+, NTFS for Windows NT/2000/XP/Vista, and other file systems for other operating systems). That simplicity is just because of that reason, it doesn't support features like ownership, permissions, journalling, and others.
If you're planning on moving the hard drive between Windows and Macintosh systems, I suggest keeping FAT32 and missing out on the ownership/permissions deal, as Windows cannot directly understand the Mac's native systems (UFS and HFS+/Mac OS Extended) and Mac OS X cannot write to NTFS, only read from it.
In case you're only ever using the drive with a Mac, I suggest formatting the drive as Mac OS Extended (HFS+) Journalised (using Apple's Drive Utility), as some programs may have problems with UFS (though, in those cases, it's mostly when the program itself is on a UFS drive, not for documents and other files)... don't forget to copy any data on the drive to somewhere else first though.
