I would have to say that the Number 2 Alliance at the Michigan State Championship (67, 217, 2612) has one of the best alliance autonomous.
I think that they actually got all 6 balls in during autonomous, 67 was in the middle moves forward and puts two in then sprints backwards to get out of the way for 217 in the far zone allowing them to score all 3 balls. I don't remember at what time during autonomous that 2612 put their ball in from the near.
Awesome planning and execution by the programmers of all three teams.
I think they did it in the match before this but you can at least see 67 and 217 doing what i described above.
http://www.youtube.com/watch?v=CWDLrB5C-N0
-Clinton-