Leave it up and running for a night, without any apps open. My N900 used to be exactly like that about 2 weeks ago. For about 2 days, it was nearly unusable. Don't know what was going postal on it, even "top" gave inconclusive results.
Sometimes I fear that "tracker" (the media database indexer)can chew up too much CPU (just had it happen again - device left alone for an hour with media player up but paused - device very slow - Ctrl-Shift-X - top .... tracker at 70% CPU for 30 seconds)