In my experience Linux has historically been very fussy about what chipsets a mobo uses. I had a mobo which had onboard wifi but Linux just wouldn't play ball. I ended up having to get a pci wifi card with an Intel chipset that worked. (In case it matters I use Linux Mint) Anyway I am considering building a 'smaller' form factor Linux system (possibly micro-ATX as I want a few pci slots, but I may go to Mini-ITX. I presume Intel is still the go rather than AMD. Are there any (smaller than ATX) mobos that WILL definitely work with Linux, and specifically the onboard wifi?