I have mine tucked inside an NMediaPC 200BA
HTPC case. The motherboard configuration has the PCI-Ex1 slot right next to the PCI-Ex16 slot which hosts my ATI Radeon HD4670 graphics card.
It's a tight fit and I'd recommend some space between the two if possible, but I've not run into any heating issues. I do understand this card does get hot and if you're really concerned, you may want to consider adding a PCI/PCI-E slot fan to blow air onto it.
Edit: I should note that this system is strictly an HTPC. The most intensive task it performs is Blu-Ray playback and HD Recording.