Applications not launching in dock or otherwise

Random programs bounce once in the dock and don't open. Mail, Safari, iChat, and several 3rd party apps are affected. iPhoto, iMovie, iDVD, Microsoft Office, Final Cut, Photoshop and others are not affected. When I try and open the program from the applications folder, nothing happens.
I tried logging in as a new user, disk utility and repairing the disk from another boot drive and nothing has helped. I also trashed preferences and even reinstalled one of the 3rd party apps and still no change. I was working away normally last night and this just happened. I had not just installed anything, in fact I had just used several of the programs and all of a sudden they wouldn't open anymore.
I'm not sure if it only affects programs that are on my dock as I haven't had time to try and open every program I have, but could that possibly be the source, something with the dock? Any help is most appreciated.

Try this:
Repairing permissions is important, and should always be carried out both before and after any software installation or update.
Go to Disk Utility (this is in your Utilities Folder in your Application folder) and click on the icon of your hard disk (not the one with all the numbers).
In First Aid, click on Repair Permissions.
This only takes a minute or two in Tiger, but longer in Leopard.
Background information here:
http://docs.info.apple.com/article.html?artnum=25751
and here:
http://docs.info.apple.com/article.html?artnum=302672
An article on troubleshooting Permissions can be found here:
http://support.apple.com/kb/HT2963
If you were having any serious problems with your Mac you might as well complete the exercise by repairing your hard disk as well. You cannot do this from the same start-up disk. Reboot from your install disk (holding down the C key). Once it opens, select your language, and then go to Disk Utility from the Utilities menu. Select your hard disk as before and click Repair.
Once that is complete reboot again from your usual start-up disk.
More useful reading here:
Resolve startup issues and perform disk maintenance with Disk Utility and fsck
http://support.apple.com/kb/TS1417?viewlocale=en_US

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