The final version of CCleaner 2.0 is still shaky, and some people is reporting it in the Piriform forums (namely, slow scanning speed). Add that the slim version is still not ready (hmmm...), and I suggest you guys to wait some days for things to settle down.
On to the applications part. My tip is untick everything. That, or go through the winapp.ini entries, going to the locations written there, and ensuring it won't delete any data you'll need. The application cleaning file of CCleaner needs a full audit to ensure it deletes everything that is fluff, and preserves everything that it's needed for the applications to operate (or at least, things that are not recreated everytime you start the application). That's why I use my own winapp.ini, to prevent CCleaner's own going berserk on my computer.