I'll "throw out" a few ideas/suggestions but I don't know how much effect it would have on your overall heat output.
1. "Green" Western Digital hard drives (assuming you believe their advertising).
2. Make sure your Energy Saver Preferences have "Put the hard drives to sleep when possible" checked.
3. Disable Spotlight indexing on unnecessary drives via Spotlight preferences' Privacy settings (to avoid unecessary possible access to those drives which would spin them up).
4. Make sure your not causing the components to overheat because of accumulated dust (i.e., regularly blow out the dust in the machine).
5. Make sure the machine's exhaust fans are not blocked (not too close to walls).
Some additional ideas:
You could also consider moving a rarely-used drive to an external enclosure where you can literally turn it off when not needed.
Drives have gotten really cheap. You could combine some functions onto a new larger drive, BUT: for good performance, you should consider creating a Boot Drive with only System, Library, Applications, the Hidden unix files like paging/swap, and the main Admin account used ONLY for administration. Move all User data files off to data drives. If you put the boot drive on a SSD, you save about half the power AND pick up speed.
The dearth of memory you have in the machine now may be contributing to extra Disk use for Paging/Swap.
Update your Mac to a 2009 model or later. They are almost twice as fast at the same GHz speed and number of processors, and the more modern memories throw way less heat.