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Onyx does the same thing (although not sure about Spotlight), It's perfectly safe. Most of this stuff is rebuilt upon restart.Clean My Mac 3 is however a potentially more dangerous app than the previous versions because it allows you to run what it calls Maintenance scripts. These are combined task programs to repair permissions, empty system caches and reindex Spotlight and Mail data bases.
Wondering exactly which binary files are unneeded? What type of files? Are we talking PPC versions of fat apps?whereas the Clean My Mac interface lists it's tasks like removing "broken" preferences, unneeded binary files etc.