I'm just using an old 250GB USB HDD with my Wii. I have it split into two partitions. The first partition is roughly 50GB in size using FAT32 with 64KB clustering. It holds all my ROMs, EmuNAND, Saves, and NGC ISOs. The second partition is EXT2 and holds my Wii WBFSs. The actual homebrew DOLs run from my 2GB SD card. I haven't had any issues from Nintendont, USB Loader GX, or any other software due to my setup.