My setup would be as follows:
1GB FAT32 (Store NAND Backup files & all USB Loader GX covers & Settings)
400GB WBFS (For games)
99GB NTFS (For anything else. I don't use ROMs or watch movies personally)
Adjust the last two to meet the requirements you need for what you like to do with your Wii. You could go for a 50/50 split with the WBFS and NTFS ... its all a personal preference.