Short bio: Computer Scientist, FOSS supporter (read more)
Tux Machines (TM)-specific
Hardware compatibility was a major issue with Linux some years ago, but it's quite safe to say that we have gone past that point. Almost all major hardware components have Linux drivers available, and they can be used without much hassle. [I remember the days 4 years back when I had installed Red Hat 8.0 and it didn't recognized my monitor as well as sound card!]
However, some hardware producers have done a better job at supporting Linux now. If you are absolutely sure that your next PC will run Linux, a brief moment of planning ahead can earn you a very powerful system that runs like a charm. So lets build a Perfect Custom Linux PC. These hardware specifications are for Linux which are fairly popular.
The motherboard, which lays at the foundation of every system, should be the first item you will need to choose.