During my research for two upcoming HTPC feature stories on building an HTPC and HTPC server I came across a couple of nice deals at Amazon (affiliate).
First up is the Apex MI-100 which is a Mini ITX, small form factor with 1 5.25 external drive bay, 1 external 3.5 drive bay and 1 interal 3.5 drive bay.
Next is the Antec 300 Case which would make a nice HTPC server case for $50. It has 3 5.25 external drive bays and 6 3.5 internal drive bays.
Antec Three Hundred Computer Case External 3 X 5.25; Internal 6 X 3.5 2*Usb2.0 $49.99 with free shipping!