applicationsdata synchronizationipaditunes
It is tedious to manually pick iPad-optimized apps from all the apps in iTunes when syncing with iPad. I just want
on my iPad, but not
You might have an old version of iTunes which does not support folders. The current version is 10.0.1 so I would highly recommend upgrading. If you have the latest then try to reinstall it. This should fix your app/playlist issues.
As for the applications being randomly added ... uncheck the "Automatically sync new apps" box if it is checked. If it is already unchecked, then hopefully reinstalling iTunes will fix this too.
Anything removed from an iOS device is not removed form iTunes.
Secondly, iTunes sync's all apps that are specified to sync, no matter whose App it is.
iTunes determines the owner to be the Apple ID, which downloaded the App.
Here is an example o the app sync window:
Here you can choose the apps to sync. And remember it will upload apps belonging to either of you, but it won't change ownership of them.
Best Answer
Under the Apps tab in iTunes (when your iPad is plugged in), you should be able to sort your applications by type, using the dropdown box above the list of apps. I believe you can then move down the list with your arrow keys and press the spacebar to check/uncheck the ones you don't want. It's not quite automatic, but I think this may be the fastest way to do it.
(I can't verify 100% the key presses here; I'm on a machine right now that doesn't have iTunes installed.)