HD become hot because there are mecanic part inside who rotate at high speed... in extreme case at 15k rpm but usual is 7200 rpm...
For cool them down, you have mainly two way...
First, on the software side, you have utilities who "shut down" drive not used after some time... it add some latency when drive is needed but a stopped drive don't heat up... perfect solution for drive who are your data archive ( film, music, photo, book, etc )...
Second method is too have a good airflow around the drive... take a look at the pic at http://www.love-from-russia.be/comp.jpg ... it is my computer... more important is the case itself... at the lower right side, you have the HD bay ( 8 hot plug drives )... the electronic back plate is with holes who allow a airflow from the front via the HD to the row of fans ( the 4 green block )... a little detail, bind properly all your cables together... loose cable break the airflow... some gadget can be usefull, like the plastic thing who lead the airflow on my two processor and memory... the 4 fans are large one with low RPM... mean low noise for a lot of airflow... original processor fan was little with high RPM ( a lot of noise )...
If your computer case don't allow a good airflow and you don't wish to buy a new case ( my case is very good but cost over 300 euro !!! ), there is some various hard drive cooler that you can buy ( example at http://www.svc.com/ec-hd-ar-bk.html )... Adding dust filter on the air intake of your case is a good move... slowdown a little the airflow but it is nothing compare to dust package inside you case after a few weeks... these dust act like a isolator and it don't help the heat exchange... and it is more easy to clean a filter that a whole case...
A interesting article : http://www.dansdata.com/gz101.htm
