I read on the Apple site that iCloud only backs up data. Apps are synced as usual via iTunes. If you set an App to ON in the iCloud Settings it backs up data only. In most cases I presume this would be preferred settings you've configured for an App. However some Apps have actual data, for example, Numbers and Pages. This would be the data iCloud backs up.
In my case, with about 50 Apps on my iPad, I've set about 5 Apps to ON in the iCloud settings. This makes for a relatively small backup, well within the iCloud.