http://www.tomshardware.com/reviews/enterprise-hdd-2.5,2609-12.html

This shows that a 15krpm 3.5 inch drive is actually cooler than a 10k 2.5 inch drive because of it's greater surface area.

So for 7200rmp drives, 3.5 inchers should definitely be cooler?

Yes, though it probably doesn't really matter. 40ish C is optimum, as far as correlation between drive failure and average temps are concerned. Either side of that, failure rate goes up. And why would you be using a 2.5" drive in a situation where you could use a 3.5" drive? They serve different purposes, and 3.5" have better capacity for much cheaper.

From my personal machine the velociraptor 10K RPM drive does sit a bit higher on the temperature scale then most of the other drives in the machine.

http://i438.photobucket.com/albums/qq102/Starforce9/Velociraptor.jpg

2.5 inchers are usb powered.

That's... news to me? They come in SATA and IDE. Yes, you can find EHDs with 2.5" drives.

Right, so like I said, they serve a different purpose.
"why would you be using a 2.5" drive in a situation where you could use a 3.5" drive? "
If you need bus-powered, it wouldn't be a situation where you can use a 3.5" drive. It also shouldn't be a high RPM drive, since that's just wasted on USB. Plus, if you're choosing between 3.5" and 2.5" based on temperature, then you clearly don't NEED bus-powered.

It's not that they're "USB powered", but their power draw is low enough to be bus-powered through a USB 2.0 port. A 3.5" drive can't be, and any external hard drive using a 3.5" drive has A/C power.

Technically a Velociraptor is a 2.5" HDD. It has a extended heatsink to make it fit in a 3.5" drivebay. 2.5" HDDs are usually for laptops, they use SATA/IDE connections...