I have two Spaces configured and I keep some Safari windows in one space and some in another. However, Mission Control only allows you to assign an application to a Space, but not different windows within an Application.
As a workaround I created an AppleScript shortcut that executes a new Safari instance:
open -n /Applications/Safari.app
This successfully creates multiple Safari instances, but the instances are still somehow intertwined in Mission Control. When I select an instance from the Dock and choose Options > Assign To > This Desktop or None, that setting in the other instance is updated to be the same.
Is there any way to launch multiple instances of an Application that are each assignable to different Spaces? (Running Mountain Lion 10.8.5.)