I liked the JLA run okay. It's the one where Plastic Man sexually assaults Big Barda. Or maybe that was just a fill-in issue. Anyway, I still can't tell whether it's funny or horrifying. But that's Mark Waid: he makes you think!
Tower of Babel was pretty cool. And the Synchronicity two-part fill-in Waid did during Morrison's run is actually one of my favorite JLA stories of all.