This has happened to me several times -- iPad 2 -- since upgrading to iOS 6. It most frequently occurs when I tap the Update All button. Rebooting doesn't cure it. However, I noticed that the clear black bar was visible on some folders. Went in, tapped the trying-to-download apps, one by one, and each then flowed through.
Seems to be some sort of bug. Until the fix arrives, I've resorted to downloading ONLY one by one.