Basically, it depends on the kind of data you are storing.
If the data can be regenerated (when a user install the app on another device, for instance), then it should not be backed up.
Otherwise, iCloud backup is OK, as the user will expect his data to be available, even on another device.
In the first scenario, you have basically two ways of achieving this...
Either you use NSURL to set the kCFURLIsExcludedFromBackupKey on your files, either you store them in a location that won't be backed-up, like <Application_Home>/Library/Caches
. Note that the second solution is the better, IMHO.
For info, kCFURLIsExcludedFromBackupKey can be used this way:
NSURL * fileURL;
fileURL = [ NSURL fileURLWithPath: @"some/file/path" ];
[ fileURL setResourceValue: [ NSNumber numberWithBool: YES ] forKey: NSURLIsExcludedFromBackupKey error: nil ];
For the second scenario, sometimes Apple reviewers think your data can be re-generated, when it's not. Then you'll have to explain why the data has to be backed-up.