I currently have 233 applications installed on my MBP (I know, I’m an apphog). I am really at the point where having that number in one directory is unmanagable, but it seems like there are some disadvantages to using sub-folders for storing applications. What is your take on this and do you have any other suggestions?
— Todd Peperkorn
The only time I have ever run into a problem putting an application into a subfolder was with Final Cut. It didn't like being there and didn't update itself properly.
But most applications are OK with it. I'd leave the main applications, like iLife, iWork and the default ones alone. Also the Apple pro apps (Final Cut, Aperture, etc). But I'd try out the others in sub-folders. Worse case, you just move them back.