Weird. On my roommate's 3GS upgraded to iOS 5.0 (I've not upgraded mine yet as my 4S is arriving today), I did not see the screen shown in the screenshot linked in the post above in the Settings/iCloud section. There were toggles for all the Apple apps, but 3rd party apps seemed to only be able to be toggled all at once, with a toggle called "Applications and Documents" or something of the sort. How do you do it?

It is admittedly, on double-checking, a bit convoluted.

Settings > iCloud > Storage and Backup > Manage Storage > [DEVICE] > Backup Options.

Indeed; it's strange they bury it that deeply. Thanks for rooting that out.