My favorite example would be "A Day In the Life" even though it's really sort of two different bits just pasted together.  A good collaboration though . . . really a three-way with G. Martin. 

I really think Becker/Fagen are a fantastic duo.  While Fagen's solo albums show him to be the main architect of their sound, the songs really take on a different (and more biting and cynical) edge when Becker is collaborating.  I don't know if Steely Dan are a rock duo, but they are a great duo at whatever it is that they do.