Jeeez! I thought this was a defrag thread!
No worries about fragmented drives in OS X.
One strange thing I've noticed though, is a tendency for the directories to get screwed up even if they're journaled. There are many reasons for this and I believe bad installers, failure to repair permissions, forced shutdowns and running newly installed applications without restarting AND rebuilding permissions are the biggest culprits.
I don't want to get flamed for this but after servicing over 100 machines, these are the most common and this is my experience.
You results may vary.
I would suggest that you invest in a good utility such as "Disk Warrior" or "TechTools Pro".This will keep your machines in peak running order with almost no problems.
Whatever you do don't run updates or do installs on a machine if you're experiencing problems with it. You WILL make things worse. Guaranteed.