In the old days we'd use Disk Utility to repair permissions, and it would often clear up this kind of problem. The commercial program DiskWarrior is often recommended these days as a "gentler" way to rebuild directory and permissions.

If your hard disk is starting to go bad, the same slowness might show up. If that is the case,I've heard that Disk Utility may have disastrous results. Doing a complete backup with SuperDuper or Carbon Copy Cloner might be a good idea before you try to rebuild the drive with DU or DW...
Good luck