Mac cleaners can really help improve the performance of your Mac and keep it protected from malware and viruses. There has always been an argument whether a Mac needs antivirus protection, however as many Mac users now know Yes Mac computers DO benefit from using antivirus software and there are many free versions available that will go a long.
Is your Mac mini PowerPC-based (a 'G4') or a more recent Intel Mac mini? This forum category is for Mac OS X 10.3, so that would make it a PowerPC-based Mac mini, but your question may have appeared in the wrong category, so it doesn't hurt to ask...
Here are some general things that apply, either way.
(1) If your free space on the hard drive is getting low, the Mac may start to 'bog down.' The system and apps use free space on the startup disk to write temporary files. If that free space is getting low, and/or fragmented into tiny pieces spread over the hard drive, it will be less efficient. So, you can look in places like the Downloads folder for files you no longer need that you can delete. If you sort a folder list view by file Size, it will be easier to spot the unneeded files taking up the most space. Free up as much free space as possible. Be sure to empty the Trash after dragging files there.
Also, clean up your Desktop. Things on the Desktop take up space on your hard drive. You should reduce the number of icons on the Desktop to only things you access all the time. If you have a large number of files on the Desktop now, you can create a new folder on the Desktop (I call mine 'Drawer') and 'sweep' all files that were on the Desktop into that folder. You can sort through it later...
(2) Run Disk Utility (from Applications/Utilities). Select your startup disk (usually 'Macintosh HD') in the sidebar. On the First Aid tab, run Repair Disk Permissions and Verify Disk. Don't be too concerned if you see a lot of messages for Repair Disk Permissions. But if Verify Disk gives you an error, that needs to be resolved before doing anything else. It could be data corruption, which can slow down overall performance and get worse over time.
(3) You can create a new admin user account in System Preferences Accounts pane. If your OS is Lion (10.7), it's called the Users & Groups pane, not Accounts. This article has the procedure for Lion, which should be similar in previous versions of Mac OS X.
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(I have a user account named 'Test User' that I use for troubleshooting.)
Log out and log in to the new user account. If things seem to run better (faster) in the new user account, you may have problems related to your usual user account, such as processes that start up automatically when logging in that are taking up CPU time or improper user preferences settings.