The Go To Implementation popup should provide some way to filter the results. (Usually I only want implementations within my project.)

I suggest this sitting at the top of the popup (like the checkbox in Go To Class):

[ Custom [V] ] [x] Project [x] Libraries [x] JDK

The "Custom" is a combobox which allows me to choose any of my defined scopes (Project and Libraries, etc), overriding the checkboxes.