I was thinking rubber for the durability and longer lasting qualities not to mention being 'sticky' when stuff is wedged against it. and I was figuring they would be resting on the backplanes from the bottom for support or am I thinking backwards?
As for thickness I was thinking 1/8-1/4" thick of semi-soft rubber and the holes being just very slightly smaller than the drives for good stability. Also if they were wedged in there a bit it would allow the rubber to bear some of the weight.
http://www.mcmaster.com/#rubber/=96tgf2
*edit* and you may be able to get the rubber cheaper if you look for alternate sources, like say, cutting up a door mat or something.
I was actually planning on doing this exact solution for a similar thing a while back when I needed to add storage to a server that had no more spots. I was going to use to sections of U channel aluminum and make 2 frames, with rubber inside the frames and holes just big enough for the drives. I would then space them apart the proper distance and rivet them to the floor of the case. And bingo, quiet, dampening hard drive storage
Only problem is I made a mistake when I ordered mats and got rubber that was too hard. And eventually the need disapeared.