Move Apple Apps from Applications folder

I'm not sure if their is a way or not. The Apps are now linked into Launchpad with 10.7 and they probably hardwired the applications folder to launchpad to ensure every app on the Mac is accessible.

There is no safe way of doing this. Apple has added extensive sandboxing and security features to Lion that prevent even the removal of some directories from ~/Library. They have locked down their apps in kind. Learn to live with it. Organize Launchpad to workaround this, use another app launcher, or suffer a cluttered Applications folder.

Why don't you just make a folder with shortcuts to your most used apps. This way you won't have to see the apps you don't use very often. You could even make another separate folder with shortcuts to the apps that you don't use very often. This way the system Applications folder will remain unmodified.

There are many ways to start an app (spotlight, dock, etc.), but this might work for you (if I understand correctly what you're trying to do)

Just tried moving System Preferences.app and while it made me authenticate, I was able to move it successfully to a folder within Applications.