It's been two years and I stand by my original answers of Ragtime and Cats, respectively, but in the Best Category I have to give a nod to The Normal Heart.
Best: Uncle Vanya (Sydney Theatre Company when it was playing at the Kennedy Center) [Sidenote: you must see this when it goes to Lincoln Center this summer.] Worst: Fuddy Meers (regional theatre just outside DC)
New York:
Best: tie between Next to Normal and Jerusalem Worst: tie between Mary Poppins and The Pirate Queen