Re: looking for an R6
The 2005 is a slightly better bike because of what oizarod115 mentioned, but can also be a little harder to find/more expensive for that very reason. If you find a deal on an '05, go for it, but otherwise, the '03 and '04 are good bikes as well.
The '05 has beefier radial brakes and upside-down forks, and I believe it also has a slightly bigger front tire (120/70) which has a slightly bigger contact patch and raises the front of the motorcycle by a few millimeters to improve the balance of the bike.
Radial brakes (vs standard) do virtually nothing, but the '05 brakes themselves are definitely better because of the slightly bigger size. Upside-down forks don't do much vs standard either, but once again the development on the forks is a little bit ahead of the standard '04 ones. The bigger front tire from the '05 fits on the '03 and the '04 without any problems, so it's no issue; if you go with the '03/'04 just buy the 120/70 when you need new tires.