There are safe reliable tested and long time programs for doing specific things, they started as a way to clean the system cache - helpful before applying system updates, or to trim log files, temp files from printers, and of course to cover all the browsers and cookies from one place.
Some of those like Panther Cache Cleaner have been around for a decade and if you use properly. CCleaner from Windows is perfectly fine if you don't want to bother with the delete history and web cache etc from inside Safari.
AppleJack from pre-Intel was run at startup in single user mode and could do 5 steps to help.
Apple made Safe Boot help and HFSX has evolved and improved - not that it doesn't need more but use what is there first and foremost HAVE BACKUPS and CLONE of your system.
Use ML Recovery.
MacKeeper - why is there a thread–å–day for this POS trash? why are Mac users prone to what is marketing and social engineered? It is "crap-ware." (I never saw a popup of it once on Windows btw). But t here are all the "Tune my PC" crapolla also.
Had you titled it "MacKeeper" you would see in the right side box "More like this" threads and solved on how to deal with and remove it. It needs a sticky like there have been with some other problems.