There seems to be a consensus as to how the roleplaying tag works; it's for issues regarding persona portrayal in games. I'd like to work out something similar for the story and plot tags. Are they synonyms waiting to happen? Does "plot" refer to something planned by the GM and "story" what emerges from active play, or vice versa? Or should both of them be scrapped in favor of something more solid?
I'd say that plot is, effectively, not being used at this time. It's only on one question, which is also tagged with the story tag. You could call it a synonym waiting to happen, but I'd consider it a non-entity at this time.
Current usage for story seems to be tied to authoring storylines for campaigns and adventure paths (i.e. what's been planned by the GM).
The main deviation here is that it also has been added to a couple of questions about storytelling (i.e. presentation) ( How do I get better at narrating/storytelling as a GM? , Co-operative story-telling mechanics).
In other words:
The plot tag is effectively unused at this time.
The story tag seems to have a strong consensus for use on questions about authoring RPG story lines. Are there tags beyond Plot and Story that overlap with it?
We may want to consider adding a storytelling tag for questions about storytelling systems (not to be confused with the Storytelling System :-P) and the presentational side of storytelling.