I'm currently looking for a CPU cooler that will fit on my ASRock Z77E-ITX motherboard.
I have a Bitfenix Prodigy and am also planning to get a GTX680 quite soon, because the CPU socket is right next to the PCI slot large CPU coolers will collide with the back of the graphics card.
I'm currently using a Corsair H70 but am wanting to get rid of that.
TBH, water-cooling is the only way to guarantee compatibility, while getting good cooling performance. Without knowing the socket clearance, I can't really tell which cooler will fit without interfering with an add-in card, as the socket does appear to be abnormally close to the expansion slot. It's trial and error.
It's entirely possible that it's a non-issue, but I can't say for certain one way or the other.
Anyway, I found this, which should help you in your quest:
Based on that, and a little eye-ball work, and the dimensions of a stock-ish cooler (Alpine7 from Arctic Coolng), I'd say keep the cooler width under 115mm, though keeping it within the socket area (90mm; 75mm between screw holes), would guarantee compatibility as well. With that said, I'd imagine most 92mm coolers would work, but 120mm will be a hit or miss, especially the high-performance ones.