I used to buy Intel boards because they were more likely to work well with the latest CPUs of the day. I've switched to SuperMicro boards for our desktops (which are mostly dual Xeon boxes) and have had few problems.

I wish they'd come with a TPM. The integration issues are frequently around the TPM and getting it recognized. It's required for BitLocker whole disk encryption which is part of our standard build. (If a machine or drive goes AWOL, we don't have to worry.)