Organize Applications Folder?

Some apps may not function or update properly if they are moved from the /Applications folder. If you want to organize, create a new folder with aliases of all your apps and arrange that one.

 

Some of the apps won't delete. You can copy apps like chess and photobooth to other places, but the originals won't delete. That is until you do some terminal commands below. keep in mind that some Apple apps will not update unless you move them temporarily back to the Applications folder, run the update, then move them back where you ant them. (stupid Apple update)

I suggest making backups first:

How to Delete Safari, Mail, FaceTime, Photo Booth, & Other Default Apps

Warning: There is no undoing the app deletion without reinstalling the individual application or Mac OS X. This will result in permanent removal of the specified applications and could result in abnormal system behavior or improper functionality. If you don’t know exactly what you’re doing and why, this is not recommended. Perform a backup beforehand, and proceed at your own risk.

Launch the Terminal, located in /Applications/Utilities/
Type the following at the command line to change to the Applications directory:

cd /Applications/

Now that you are in the Applications folder, you can start deleting apps. You will not get a confirmation of the removal, the app will simply be deleted completely. The following commands will only work when used in the /Applications/ directory.

Delete Safari
sudo rm -rf Safari.app/

Delete Mail
sudo rm -rf Mail.app/

Delete FaceTime
sudo rm -rf FaceTime.app/

Delete QuickTime Player
sudo rm -rf QuickTime\ Player.app/

Delete Stickies
sudo rm -rf Stickies.app/

Delete Chess
sudo rm -rf Chess.app/

Delete Photo Booth
sudo rm -rf Photo\ Booth.app

If you’re comfortable enough with the command line, you could supply the full application path with /Applications/Appname.app but considering the potential for catastrophic error with sudo rm -rf we used the safer method.

 

You can also do a Get Info and then change the sharing and permissions settings. I've moved Game Centre and Chess into a Games folder by this method and both run.

You will have to put them back into the Applications folder before applying a software update however or this will create a ghost version Applications and things can get messy.