My personal favorite Dylan song is "Subterranean Homesick Blues." The video that goes along with it is very cool.
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I'll have to go with "Positively 4th Street", because these lyrics make me laugh every time:

"Yes I wish that for just one time, you could stand inside my shoes
You'd know what a drag it is to see you"
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"Tangled Up In Blue" Great song!
http://www.youtube.com/watch?v=mvBkbPEoeAI
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I love the ones posted so far, but my personal favourite is "One Too Many Mornings"
Source(s):
I first heard this song covered by the great San Francisco band, The Beau Brummels. The 2nd post on this site has the better sampler of their version: http://mog.com/music/The_Beau_Brummels

And as Dylan performed it live in 1966:
http://www.youtube.com/watch?v=MgwCu5Vl1UU

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