Wow... when I saw the headline, I naturally expected yet another puff piece extolling the genius of Nathan Myhrvold to all who will listen. NPR gets some serious kudos for proving me wrong.
The Planet Money / This American Life team brings tears to my eyes they're so good. While I won't say they don't have any sacred cows (I don't know that they do or don't), they're certainly not afraid of skewering many articles of faith.
I've also been a long, long time listener of Terry Gross's "Fresh Air", and it seems to me that it improved markedly during the aughts by tackling serious political issues. I don't know if that change is my perception or the program (my first memories are of its coverage of the Clarance Thomas Supreme Court nomination).
On The Media is also usually pretty good, though it can be a little uneven.
I have to say that the anchor programs -- Morning Edition / ATC, and Talk of the Nation -- have lost much of their edge. ToTN particularly seems to play to drama rather than fundamentals (its Political Junkie segment especially, starting with the intro soundbites all of which are sensationalistic).
APM's financial programs (Marketplace Radio / Marketplace Money) wouldn't know sound financial advice and perspective if it gave them a black eye. Internet sources rule here, largely on the sacred cow basis (and TAL/PM blow them out of the water).
But overall, it's among the better of the large broadcast organizations.