Whatever- Godsmack, Voodoo (Drop C)
Your Disease and Click Click Boom- Saliva
Too many RATM to name here
Bored and Shove it- Deftones
Drift and Die- Puddle of Mudd
Mudshovel - Staind
The Red, The Clincher, Send the Pain Below and several others- Chevelle ( Drop C)
Pure Massacre - Silverchair
Hey Man Nice Shot, Picture - Filter
Casual Affair, Open up your eyes - Tonic
Sound of Madness - Shinedown
I'm sure I am forgetting a bunch. And for the record, Drop D to me is Drop C#. Plus we do a lot of these in Drop C and some of these that should be Drop B and Drop C we do in Drop C#. You could pretty much do all of them in Drop D if you wanted.
Them Bones, in some of the live versions Jerry starts the riff with the traditional D chord fingering on the 14th fret with the open top 3 strings and slides it down just in time to bar the first fret to mimic Layne's yell. I found that doing that really helps to compensate for the lack of vocal chops when I use to play it.
All of the usual suspects have been mentioned already.