OnyX is a utility for Macs that allows you to check the integrity of your startup files, as well as configure some hidden parameters of your system. There are OnyX versions for the latest releases of Mac OS X (and they are not cross-release compatible) so you have to download the appropriate version. The download is free and OnyX installs easily as long as you allow installs from non-App Store sources.
OnyX can verify your startup disk and the System file structure. By itself, this is a useful function in case of system issues. However, OnyX does more, allowing you to configure some parameters not typically accessible for the Finder, Dock, Safari, Mail, and other apps. You can also use OnyX to delete disk caches and logs. The OnyX interface features dialogs, which look a little overwhelming but actually are designed to give you control over all the parameters OnyX can touch. The learning curve is not trivial, but not complex, either.
The flexibility OnyX offers is remarkable, and while you can't get OnyX from the App Store, it is available through the developer's Web site. Since OnyX has been around since 2003 and there's a constant update process from a dedicated developer, this is one of the more useful utilities we've encountered. Recommended.