Reading through the developer docs, it seems that developers have a number of temporary and permanent directories that they can keep stuff in.
They're encouraged to keep stuff that can be re-downloaded in temporary directories which are not backed up to iCloud.
Take iTunes as an example. iTunes would back up your preferences, settings etc. to iCloud, but it wouldn't back up your music, because it's assumed that there's another backup of that elsewhere (on your computer).
As another poster said, you can drill down into the iCloud settings and see exactly how much data is backed up for every app.
On my iPhone I've chosen to back everything up, and that's taking 750MB.
On my iPad, my photos were going to be 500MB and my movies (which I keep in GoodReader) were going to be 6.5GB. Since I have backups of both of these on my Mac, I didn't want them in iCloud so I deselected them. All my other apps now back up in just 650MB.
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thanks can you backup to icloud -and- your mac? imagine they may get out of sync at some point?
Yes, in iTunes you can right click to get a drop-down and manually select a backup.
It may be easier and quicker restoring from this backup over USB if you want to migrate to another phone in the future.
These backups will get out of sync unless you regularly make a manual backup on your Mac - but that's your choice. The iCloud backup should be very up to date, and the Mac backup kind of a 'backup backup'!