Choosing the right motherboard is a twofold problem when it comes to VFIO. Not only do you need to carefully select for the right bios features and I/O, but you need to know how well the PCIe slots are isolated via IOMMU.
The problem is, no vendor lists the IOMMU layout on their boards, and the only information you can generally find is scattered in forum posts and may be years old. Furthermore, certain chipsets have quirks that, while known to community veterans, can stop newcomers in their tracks. Here, we provide personally (or in some cases community) vetted known working models for the range of products we recommend. If the part has issues that need working around, check the entry for asterisks, and reference them below.
UPDATE: as of AGESA 0.0.7.2 Mainstream Ryzen Motherboards Break VFIO entirely.
[*] – ACS needed in some cases: generally this workaround means that the board functions fine for regular use, but the cpu-specific lanes may not isolate properly. If you want a 2 dGPU build instead of using the iGPU or a chipset slot on these boards, the ACS Override Patch will generally be needed.
[**] – ACS needed in all cases: This board was chosen for price, not performance or compatibility. The IOMMU groups will not be functional for 1 GPU passthrough builds without the ACS patch.
[†] – CSM Toggle/Slot Swap: For these boards, the CSM module needs to be turned on/off in the UEFI to allow the host gpu to work properly, or GPUs need to be rearranged so that the system designates the correct GPU for boot.
[‡] – EFIFB off: the efifb option needs to be disabled for the host GPU to boot properly from the chipset slot.