I have been a fan of OnyX (http://www.onyxmac.com) for some time now. As the OnyX website claims:
OnyX is an all-in-one system maintenance tool and optimizer. It is a very simple and light application that comes with a variety of maintenance tools that can be run to make sure that you are enjoying your system at its fullest.The first scans that OnyX will make automatically when you run the application for the first time are a S.M.A.R.T status check of your hard drives and the analysis of your startup discs. If the application detects any problems, it will prompt you to carry out a reparation task.
Not everything that OnyX can do deals with hard drives, though. In the main window, there are five categories. The first one is hard drive analysis and restoration, but the following
ones allow you to repair the permissions of your system (a common problem with Macs), clear your browser settings, cache, passwords, etc., delete application, user and system caches, and more.
An array of more advanced features is also available. Those allow you to hide or show volumes, repair discs, run custom scripts, among others. OnyX comes with extensive help and it
even includes a glossary with the information about many tasks.
I have been running OnyX on a regular basis to keep my Mac Mini “clean” for a few months now. It does take several minutes to run, as it scans the entire hard drive, so the larger the drive, the
longer OnyX will take to run. I have been using the Automation option, taking the default settings, which will run several tasks without needing you to tell OnyX to “Continue”. I always recommend that you back up your Mac before running any program such as OnyX, but I have had no issues with it thus far. The latest version of OnyX, 2,9, is compatible with OS X Yosemite.
This is a tool that I recommend everyone install and run on a regular basis.
NOTE: (1/14/15) I have seen Onyx affect Safari on a couple of occasions, leaving the Sharing icon with “No Services”. I had to apply a fix from the command line to restore them.