In Gmail, a user can tag emails with a star. If you don't already use this, you should really look into it. Starring an email allows you to then use the "starred" search function, which pulls up only starred emails. It's a wonderful feature.
My suggestion is to add a star. Add two stars or three, even. The more the starrier.
The idea is simple. Of the emails which require flagging with a star, some of these are more important than others. Some, you merely want to flag, a little twine around your pinky finger reminder. Others, like a plane ticket receipt, you might want to double flag for easy access.
I predict two-star flagging will be a thing of the future. :)