I want to find a way to delete all the useless files: binaries, log and cache files, duplicate files and app's leftover.
How can I do that?
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Verify the Startup Disk and the structure of its System files, to run misc. tasks of system maintenance
Configure some hidden parameters of the Finder, Dock, QuickTime, Safari, Mail, iTunes, Login window, Spotlight, and many of Apple’s applications
Delete caches, to remove a certain number of files and folders that may become cumbersome, and more.
Removing duplicate files is not supported by Onyx.
I use Macaroni by Atomic Bird http://www.atomicbird.com. Cost $10. Installs as a login item, with a pane in System Preferences. Automatic daily, weekly and monthly cleaning.
2014: I would also recommend "Duplicate Detective", currently $3 in the Mac App Store. It finds files with duplicate hash values, not relying on file names or just file sizes alone.
One of the oldest and popular app is CCleaner. It is most popular app for PC. And it works perfectly on Mac too.