There are a raft of utilities that provide a front end for the built-in Unix system tasks. Some are free, some cost a little bit, either through a purchase or shareware fee. Cocktail is a great example of a paid app that is very complete but it's not free. OnyX is a good free app with similar capabilities.
IceClean does a whole basket of system fix-ups and the price is zippo. We took a look at IceClean a couple of years ago, and it's been updated for Snow Leopard. Everything from triggering background maintenance tasks that normally get done in the middle of the night, to permission repair, preference file verification and cache clearing.
The app also has some network utilities for the more technically minded, like traceroute,, netstat and whois. The app can also force the trash can to empty, force eject optical media, and it can clean up many problems with Spotlight. There are a lot of other functions and you can check them at the IceClean website. Remember that like any utility, it's doing some deep digging into the Unix core of Mac OS X, so it isn't a good idea to force quit the app when it's running. It doesn't offer a lot of feedback other than a spinning gear, so caution is the word of the day. The current version supports Snow Leopard, while version 2.5 supports OS X 10.4. All these apps have some overlap, and most of them have some unique features. Check them out to see which ones best meet your needs.