I would say DRIVERS... as it seems that vendors don't take so seriously the Linux...
Also, another problem that I faced recently: I have an ASRock m/board (H67 chipset) and because some bug(*) of the BIOS , the system could not properly resume after suspend, the support insisted that there is no problem 'under windows' !!
Ridiculous but this is the reality ,most m/board vendors does not even give an f for Linux.

Another issue that I have is the NTFS implementation is poor, you cannot even defrag/repair NTFS volumes...
(for various reasons I have to work with external NTFS HDDs, so a lot of times I need a PC with windows to repair/defrag the MTFS filesystem)




(*) finally the bug fixed automagicaly, as they updated the BIOS and added Ivy Bridge support...