A nice collection of covers is listed over at Guitar Woman: Female tribute to Tom Waits - vol. 3. And if you've missed vol's 1 and 2, you can find the track lists here.
The upcoming debut album from N.A.S.A. (North America/South America) - a band made up of Squeak E. Clean and DJ Zegon - boasts a track where Tom Waits finds himself in the company of Kool Keith. The song 'Spacious Thoughts' is streamed in Pitchfork Media.
You can also hear the track over at ANTI, on the blog.
On Atmosphere's album When Life Gives You Lemons, You Paint That Shit Gold you can find Waits beatboxing on the track The waitress.
Paul Westerberg has released a mini-album called 3oclockreep featuring some Waits input: a sound collage contains about 10 minutes of outtakes from Tom Waits in the studio with the Mats (aka The Replacements), circa 1989. It's available at Tune core
And I'll leave you with two video's. The first one is M.I.A.'s version of Way down in the hole.
The second one is Ambulance, a D-Sisive track from The Book, with some Waits samples.