I second the Bert/Maria imaginary airplane ride - this was always one of my favorites - just the way Bert looked in his goggles - Maria constantly yelling "look out for the cloud!" and that way too cute and perfect kiss Maria gives Bert on the nose at the very end timed to the tag music.
and the clip i totally have wanted to see again for decades - a song about Surprise sung by the street cast (it also had Grover in it) that's not been shown forever not only due to the young age of the cast but it also was before Will Lee passed away - this was the most amazing song that just went in all sorts of crazy directions - doors opening to brick walls, Groucho glasses, lots of pies in the face (it ended with the cast singing "Surprise!" as a flower on Big Bird's chest turned out to be a final pie that flung itself towards the tv screen.) This would probably be my holy grail of old bits i'd love to see again!
And although i'm willing to bet it's on sesamestreet.com (and if it isn't it should be) i would love to see the offical youtube channel put up the classic "Visual Thinking" routine between the hipster and the square talking about shapes ("Do you know what a square is?" "I know WHO a square is!")
...and more than just adding clips, i wish more than anything they would add a search feature where one could look up clips either by year or even better the episode number it first appeared in.