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did you import settings or prefs from another machine and maybe those are causing problems? Try a reinstall? (Not archive and install)
If you have 10.4, check the activity viewer and see if a process called mds or mdimoport are busy sucking up all your cpu cycles. Those are spotlight related items and you might be having trouble with that if you have a bunch of server volumes or other things mounted. Need to tell spotlight to leave those alone.
Have you tried dumping all your caches, including spotlight related data and waiting until spotlight has finished indexing your HD before using the computer?
It does sound as if something is really messed up on your machine so a reformat, reinstall, wait for spotlight to finish indexing, and then starting to reinstall your software seems like the only possible solution at this point although I wonder if that would even help.
Are there any clues in the console or system log as to what process might be causing all the problems?
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