I've got books in iBooks. PDFs are missing but that's by design. It's in the release notes . . .
Performed a settings reset for another issue with missing album art and I now have the opposite scenario from you. PDFs are there, but my books, although appearing, have the ready to download from iCloud logo.
Still, that's an improvement.
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There are some apps mentioned as faulty on this thread that have always worked for me on a 4S including;
Draw Something
Reminders
Skype - works with exception of "Recents" list
USA Today
YouTube
EDIT - Just noticed that Yelp works fine except that you can't add Photos from the Camera Roll. Updated the original list.
. . . So the question is do apps get better during the new betas?
I know we really don't know I guess if anybody remembers of they do or not . . .
The trouble with any staged Beta is that some apps may work with Beta 1 and others are fixed by updates e.g. TuneIn Radio.
When Beta 2 rolls out, however, chances are high that something else will change and a few apps that previously worked will fail.
This will continue all the way through the Beta process and beyond, hence why there are regular updates every day on the App Store for bug fixes.
One thing that can be said, however, is that the number of apps failing should be at its highest on Beta 1 barring a major OS change by Apple during the development.