HT1338: OS X: Updating OS X and Mac App Store appsLearn about OS X: Updating OS X and Mac App Store apps
Too little information.
Are you logged into the correct user account?
What have you changed recently?
Have you reinstalled or updated something?
Is everything broken or just Mail & Photobooth?
Have you checked the Trash?
Does Spotlight find them?
Are there any other error messages you have seen or weird behavior recently - things shouldn't disappear unless the disk is damaged or failing - you usually get warnings or messages as this happens.
Are you using multiple hard disks, could one of them have an older or newer copy of the applications? Disconnect them, reboot & try again.
Have you looked for just the applications or have you looked for the data too?
Mail stores the messages in 'Your Home/Library/Mail' - is this empty?
Photo booth stores it's files in 'Your Home/Pictures/Photo Booth'
Check the above locatons in the Finder are they empty?
Do you have a Time Machine backup or a clone of the system?