Subfolders inside the Applications folder - particularly separating the Apple Applications are not a good idea as they interact with one another and need to see each other at the root level of that folder to do so.
I installed Safari 3.0 and spent the next hour on the phone with tech support. Seems it is causing the system to crash.I was among many to call with the same problem. It would not allow me to do anything until I used the reinstall disk. Funny thing is it works perfect in Boot Camp with Windows.