I can tell you about my only experience. I have used a Q-tec 750...something for a while. It had a plastic case and a thin fan under the HD. The fan sounded too much for me and was a non standard blower type. I ended up unplugging it when I didn't use it. Since the HD just would sit there on the shelf for most of the time I decided to check the temps without the lid.
I used a standard IDE cable instead to get the temps and did some testing:
Lid on, fan on: 45 degrees
Lid on, fan off: 56 degrees
Lid off, fan off: 46 degrees
The choice for me was easy, I used the latter and it got really low noise when used with a 120 GB Seagate 7200.7. I just put the lid on with some tape the few times I moved it.
So, don't just look for a fan when buying, they can be both noisy and inefficient and possibly unnecessary like in my case. Ok, a 11 degrees drop isn't that bad for such a small fan, but a 80 mm fan at 5 V does a better job and makes LESS noise (big difference), so we're not talking about a standard fan. If you have to move the HD a lot then it's another story.
Maybe check out metal cases, they should give some good passive coolig if designed properly. Here's a review of an internal enclosure, and it shows that it cools passively quite good (2 degrees rise).