I love games that incorporate a time shift so that you get to explore the differences between areas during different time periods, such as in Zelda Ocarina of Time, and the Lanayru Desert/Mining Facility part of Zelda Skywards Sword, which is why if I could only pick one level, Click Clock Wood would be my absolute favourite from Banjo-Kazooie. But I also love Rusty Bucket Bay and Mad Monster Mansion for all the little hidden rooms in the ship and house. And Treasure Trove Cove is so cheery that I can't help loving it (not to mention I will NEVER forget the way my sister screamed when she dived unsuspectingly into the water to grab that blue Jinjo only to be met by Snacker - she has had a phobia of sharks ever since
). All of the levels of Banjo-Kazooie are so great that it's hard to pick just one.
In Banjo-Tooie my favourite is Witchyworld, because I love theme parks and creepy carnivals. Don't really have a runner up as the levels didn't seem to be as memorable as the Banjo-Kazooie ones. Maybe Grunty Industries, but those Tintups made it to frustrating because you couldn't explore rooms properly while running from them. Oh, I really liked the town part of Jolly Rodger's Lagoon too.
I didn't ever get that far into Donkey Kong 64, I really should go back and play it one day.