A traditional wind instrument created by Australian natives.  I'm looking for any VGM that uses this instrument.   Please feel free to add to the list!  So far, off the top of my head, I can only think of four pieces:

"Hydra Marshes" - Chrono Chross/ Yasunori Mitsuda
"Earth Temple" - Zelda: Wind Waker/ Kenta Nagata
"Oh Yeah" - Killer Instinct/ Robin Beanland
Goldwood level - Jet Force Gemini/ Robin Beanland

Edit - added the last two tracks.

You don't hear this instrument too often in VGM, but it has a very distinctive sound that can be quite interesting when used well, notably for tribal and desert themes. For the moment, I can only think of two games I've heard it in, but if I can remember/find more, I'll post again.

The "Uhndrashi Plateaus" themes - Shadow Madness / Brad Spear
"Spirit Bog" - Small Soldiers / Michael Giacchino

There might be a few tracks from Akuji featuring it as well, but I'd have to check the music again to verify.

"Din Don Dan Dan" from the Ragnarok Online II soundtrack uses one, I believe.

Try "no bird" from Lumines remixes winter.

I'm not positive, but I'm pretty sure I remember didgeridoo being used in Uncharted: Drake's Fortune.

Tamamayu Monogatari OST has a lot of tracks using the didgeridoo. It's also the best "jungle atmosphere" soundtrack I've heard, even better at setting that kind of mood than the DKC soundtracks. Highly recommended.

Thanks guys!

I don't know if you're still looking for more tracks, but I just noticed that "The Shaman Rides" from Sly Cooper 3: Honor Among Thieves features didgeridoo prominently.