I can understand why Tom's has to do this style of article over and over and over and over and over again - computer hardware is constantly advancing and by the time they print something, its out of date.
However, I challenge Tom's to at least once mix it up a bit. Instead of the best gaming rig, do these build offs for a different application. Myself, I already have my gaming rig... now, help me improve my HTPC. Try to build the best darn computer you can that also has to be power efficient, quiet, and handle full BD and HD-DVD playback with full audio.
As to including the OS, I almost always buy the OEM version. $140 versus $300+ makes a big difference. Unfortunately, OEM is technically tied to the hardware for which you buy it (yes, I know you can get around these - but lets keep these above board). So lets go under the assumption that the builder either a) owns a mass-manufactured computer that has hardware-locked OEM software installed (like a Dell, HP, Compaq, Gateway, etc), b) this is their very first computer, or c) they want to keep their old computer as-is and this is an additional computer.