Quick update on this, thanks for all your input.
I went for the Phanteks cooler in the end. It fits in there nicely and doesn't get in the way of the first PCI-E slot. There isn't a great deal of space though, so I don't think a cooler like the BeQuiet would have fitted.
The Phanteks is very quiet and performs well, so I'm going to be experimenting with some overclocking today. Already got up to 4.2GHz with no problems.
Cheers,
Ricko