Coolermaster make a cage that allows you to fit 4x 3 1/2" drives into 3x 5 1/4" bays which has a 120mm fan for cooling. That at least doesn't seem like a complete waste of drive bays if you have a few extra hard drives (and should provide pretty good cooling with not a huge amount of noise.)
I'll be installing one tonight in my file server so I should be able to give a better review tomorrow.
Other than that most of the coolers I've seen are passive or have 40mm fans at best and I'm not a great fan of 40mm fans, they tend to either make a lot of noise or not actually accomplish much.
Vantec make a couple of coolers with larger fans which I would guess would be a little more effective, but you'd probably want to check some reviews...