I often see a yellow start near the methods, and some percentage in Eclipse Luna's intelligent code completion:
What does this star and the percentage mean?
Both the star and the percentage are added by the Intelligent Code Completion.
These suggestions are based on context and code analysis (data mined) of similar situations. The percentage is presumably an indication for the confidence of that suggestion.
Protected methods (which was the explanation suggested by Ted Hopp) are in fact indicated by a yellow diamond with rounded corners, similar to the icon in the outline view.