Use Wii backup manager for Wii games, put them in a folder named wbfs all lower case in the hard drive root. Some USB loaders like the game in a folder with the game name and ID like
Usb1/wbfs/Super Mario Galaxy[SP4E01]/galaxy.wbfs
For GameCube it depends on the loader, for Nintendont the game should be named game.iso, inside a folder with the game name, and that folder in folder named games in the HD root. So...
Usb1/games/Super Mario Sunshine[SMNE16]/game.iso
FAT32 has a file size limit of 4gb so you will need to use Wii Backup Manager to split larger games.
On "that iso site" someone had a program that will convert a wbfs portion to Fat32 for you without taking everything off and putting it back.
You can get game ID at gametdb.com
Forgot to add, the partition needs to be primary and active, and if you have multiple Fat32 needs to be first in the partition table. Also I think Nintendont requires the disk to be MBR not GPS and 32k cluster size