On top of the advice given here, I'll point out that OS X has maintenance scripts that are run daily, weekly and monthly that do a bit of cleaning (more info here). The only downside is that they run during the middle of night so if your machine isn't on, they won't run. That said, you can run them manually and I get the feeling that OnyX runs them as part of the automation process (daily, weekly and monthly log files on my machine all show that they were last run when I last ran OnyX).