Safari is a huge factor in Mac mini beachballing issues. It hogs a bunch of RAM. 2GB really isn't enough for Snow Leopard.
Open up Safari and go to Safari -> Reset Safari...
Reset everything. When you open Safari next and go into your bookmarks, it will ask you to "add webpage previews now?"... Hit ignore or cancel or whatever. Just eats up space.
Go to Safari preferences and make sure that neither new windows, nor new tabs open up with Top Sites. Remove it from the bookmarks bar as well.
Open up Terminal and type this in (disables Top Sites Completely):
Code:
defaults write com.apple.Safari DebugSnapshotsUpdatePolicy -int 2
Then download
Onyx.
Go to the "Cleaning" section and clean out ALL the catches. Then restart the mini.
Then go to the "Maintenance" section verify/repair permissions.
Restart.
Your mini should run A LOT better after doing all of this.
Oh and are you running multiple accounts on your mini? If so, I would disable fast-user-switching... 2GB isn't really enough to support it. And if you use VLC, I have another suggestion that will make a HUGE difference.