I use iCleaner Pro (bought it at one point, hate the ads). One of the first set of tweaks I reinstalled when the 9.0.2 jailbreak dropped.
There was some initial issues that people had with iCleaner back then and I did experience a bootloop after cleaning caches at one point. However, that resolved back to Flipswitch and Activator at the time for me. Although iCleaner Pro did seem to act somewhat glitchy.
I left it installed, but didn't use it really and the dev later updated it. In the few times since then I've needed it (to troubleshoot problem tweaks and delete pref files as well as clean caches) it's been solid.
My understanding now is that it's got some sort of new stuff that will prevent things belonging to the new jailbreak from being tampered with by the user.