... I can't answer this with only one or two books!
Best Flash book (as both a favorite and in terms of quality): Return of Barry Allen (2nd place: Blitz)
An utterly fantastic character driven story that exploits the lore and continuity of comics to creat and epic tale of finally emerging from a mentor's shadow.
Best Teen Hero comic: Young Justice - the whole series.
To me this thing beautifully uses humor, drama, and action to tell a great introduction story that manages the hard task of balancing beloved characters who have their own solo books.
Best Superman story: "What's so bad about Truth, Justice, and the American Way?"
Personally, I think this is the strongest reconstruction of Superman as a hero, and it does it all with the Post-Crisis Superman. Suck it, Silver Age.
Best Batman book: Too many to count, it honestly depends on my mood.
Best Robin book: the first Robin miniseries.
Does a great job with introducing Tim Drake, using Lady Shiva, and introducing a great antagonist in King Snake.
Best Batgirl book: the Cassandra Cain series up until the death duel with Shiva.
See above, but with the *best* Batgirl.