This is something that's incredibly helpful for working with applications that absolutely must be on a live server -- such as Facebook games. It's really easy -- but I personally had a whole bunch of things go wrong in attempting to get it working. Credit for figuring out the pitfalls goes to Warren Eng, one of my developers.

Steps:

• Make sure your app is set to allow debugging. In FlashDevelop this is "Debug" mode, instead of "Release".
• Close all web browsers.
• Set Flash Builder's default launch browser to Chrome.exe (Window -> Preferences -> Flash Builder -> Profiler -> Player/Browser) -- Note: I have no idea why Chrome works here, but when I use Firefox it fails. Chrome works flawlessly. I've given up trying to understand why -- and besides, Chrome has a great task manager for monitoring memory.
• In the "Profile External Application" window, add your application's URL to the "Launch selected application" box. (i.e. http://apps.facebook.com/myGame/game/)

At this point your Flash/Flex builder should ask you to suspend/resume your application, and when you resume it you'll start getting all that juicy profiling data that you want.

Good stuff!