It kinda depends on what version of windows you are running. If you are running XP or 2000, you can use either NTFS or FAT32. If you are running one of the 9X versions then you must use FAT32 (I guess you could use just plain ol' FAT, but that would be retarded).
Also you might want to note that if you place file from your Mac onto a NTFS or FAT32 file structure, you will have these strange .#RES files appear after your Windows box accesses the drive. I'm not sure what they are, it has been purposed that they are the resource fork to the file. Anywho, this can really cause problems, because your Mac can forget what to open the files with and I haven't found any way to merge the two files back together, thus they are totally useless.
If I were you, I would connect the firewire drive to the Mac, format it using the Mac file format (sorry can't remember what is is called) and use Windows File Sharring when you need to access files via the PC.