If it happens again...
Open Console in Utilities & see if there are any clues or repeating messages when this happens.
One way to test is to Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, Test for problem in Safe Mode...
PS. Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive
Reboot, test again.
If it only does it in Regular Boot, then it could be some hardware problem like Video card, (Quartz is turned off in Safe Mode), or Airport, or some USB or Firewire device, or 3rd party add-on, Check System Preferences>Accounts>Login Items window to see if it or something relevant is listed.
Check the System Preferences>Other Row, for 3rd party Pref Panes.
Also look in these if they exist, some are invisible...
There was the problem in safe mode.
Lets see here, i have these:
Flip 4 Mac
And thats about it. I could not find a few of those folders you mentioned, but I found these, and here is whats in them:
Library > Launch Agents > (an apple adress book sync and some adobe reader update code)
Library > PreferencePanes > (absolutly nothing, this seems very strange)
Library > Preferences > Lots of mismatched apple code and adobe, byhost, macromedia, and microsoft, and SMB help data, along with a LOT of mis-matched microsoft code and "widget" code.)
Also uninstalled Flip4Mac, but there seems to be a few files of it still on here.
I had a similar issue with a wireless Logitech mouse. The freezes was due to the Wi-Fi interferences between the mouse and the Logitech unifying USB mouse receiver attached to the mini. Try to attach the mouse USB receiver with an USB female cable a bit away from the mini (10 or 15 cm should be fine). Worked for me.
Tried this on 2 mouses, an apple track pad and another non-apple mouse (like the one 3nd described)
I updated to Mountain Lion, still getting the problem. But it is not as fuequent on the track pad anymore. I'll try a SMC reset and repairing the permissions again. I still think it might be some preference pane issue, or mabye a virus (but i highly doubt its a virus).
PC repair store just opened up down the street might go ask them some time.