Yes (but you might need to format the drive with GPT partition scheme)
But how much space do you actually need for GC/Wii games? 3TB seems like a bit overkill. I have about 150 Wii games and a handful of GC games on a 500GB HDD with lots of space left over. I could fill up the rest of the space with GC games and I'd probably have just about every GC/Wii game I'd ever want to play.
GC games are pretty small so you could probably fit the entire collection minus duplicates on like 1TB or less (and how likely are you to ever want to play all of them anyway)
Wii games are a lot bigger but most of them were shovelware anyway.
So I'd say 2TB would be pretty generous for GC/Wii games.
For the record, Wii games can load from NTFS which saves having to split up the .wbfs games and you can store large files like movies etc. on it if you have lots of free space. So if you're going the 2 partition route you may as well make one of them NTFS.