I found a video on youtube which has, to my knowledge, a couple minutes of unseen Banjo-Kazooie beta footage! Well, at least footage that hasn't made it around the internet.
http://www.youtube.com/watch?v=ttZmyB0xu2s
It shows clips of the Musical Jam intro, Giant's Lair(new!), Mumbo's Mountain, Treasure Trove Cove, inside the Sand Castle, Banjo's beta jiggy dance, and more.
[Edit]
Cybernet video found by Coolboyman. The main thing to point out here is the bull near the lighthouse in Treasure Trove Cove:
http://www.youtube.com/watch?v=3evFP0NjUgQ
Also, some unrelated E3 videos show that the theme for Click Clock Wood was in the E3 version of Banjo-Kazooie as well.
Listen closely:
http://www.youtube.com/watch?v=IgOfJalW_tQ
http://www.youtube.com/watch?v=YWfyexueuc4