Glee is serial in its format, and therefore the episodes tend to bleed into each other.  Barring a few exceptions (the Madonna and Lady Gaga editions), they do not conspicuously stand out from the other episodes immediately before or after.  Thus, my criterion for picking the best Glee episode of the year was based on which one featured the best Sue Sylvester moment of the year.  The scene in Principal Figgins’ office in which Mr. Schuester took Sue to task over the issue of many of her Cheerios failing Spanish (“Oh, Will, we all know about your devotion to that dying language”) was enough to make “Throwdown” an instant classic in the span of two minutes.