2. Cloud Cuckooland
3. Hailfire Peaks
Witchyworld was by far the best, it had so many things packed into it and such variety with four sections and the big top in the middle with one of the best boss fights. The only thing that sucked was the transformation, but whatever.
I liked Cloud Cuckooland for the simple fact of how it was so random and had so many things to do and see.
Hailfire peaks was cool simply because of the idea, but what would have been amazing would be to have Banjo take one side entirely and Kazooie take the other, with a Split-Up Pad in the middle. It would have been hard to do, yes, but they could have done something amazing with that idea.
Like everyone else, I absolutely hated Grunty Industries, but just because of how complex and confusing it was. I loved Banjo-Tooie on N64, but when I got to this level on XBLA my motivation for playing dropped to zero.