Consistency from year to year is a little tougher to gauge, since The Big Goal In Autonomous Mode isn't necessarily the one that teams choose to do. (2005 comes to mind.)
That said, some favorites come to mind:
25 in 2006: These guys had it nailed. When folks at New Jersey started aiming their autonomous at them, they implemented a delay to throw them off again. It's definitely a contributing factor in their undefeated streak stretching from New Jersey through Vegas and all the way to Saturday in Atlanta.
111 in 2003: StangPS was ahead of its time. Chart out your waypoints, download to the robot, run. In a game where autonomous execution was a huge advantage, you couldn't beat it.
254/968 in 2006: It was a simple autonomous--drive forward and shoot. They couldn't pan, due to the design of the robot, but its ability to abort the run based on sensor feedback (such as, say, due to a hit) made it more powerful than similar teams' designs.
1902/1369 in 2007: The keeper wasn't as big as some years' autonomous goals, but 1902 (and, to a lesser extent, its twin 1369) were able to execute beyond compare, all the way to Einstein in the former's case.
1114 in 2008: To steal a label from
another Canadian, the Simbots of this past season were The Excellence of Execution. I don't think there was anyone more effective at both lines and balls.
1519 in 2008: Reports of Speed Racer getting
two laps in autonomous at some off-season events should send chills down the line of everyone.
910 in 2007: Two keepers in a match where most matches were lucky to even see one attempted. I don't know if it would've stuck as well in the regular season, where autonomous countermeasures are more likely to develop, but the feat is undeniable.