Gosh! What a question! There are just so many great songs that the man has done, that I cannot in good faith put them down to a top 20, let alone one.
But I will try all the same. "Hurricane" is an absolute classic, but I think it is probably just shaded by "Like A Rolling Stone"
It really depends which Dylan you are talking about, as he changed style and persona virtually from album to album, with the vast majority of it successful.
I'm very bad when picking favourites. I can't pick a favourite book, or author, musician, or overall song. Even with film, the choices are somewhat more clear cut, but are down to a field of three or four.
Now you've got me all worked up and flustered at 0300 over this question...
Crimson flames tied through my ears rolling high and mighty traps
Pounced with fire on flaming roads using ideas as my maps
"We'll meet on edges, soon," said I, proud 'neath heated brow.
Ah, but I was so much older then. I'm younger than that now.
When I was a teenager, I liked this song just for the sound of it.
Now that I'm in my thirties, I like it because I can relate to it.
Another of my favorites was "Chimes of Freedom", which I didn't discover until Bruce Springsteen released a live cover of it in '88.
And then there's always "Mr. Tambourine Man". The best Grateful Dead tune that the Dead didn't actually write.
William Shatner recorded a so-awful-it-was-funny version of "Mr. Tambourine Man" back in the late 60's/early 70's, which was the model for all those songs he performed on the Priceline commercials. I was surprised how many people weren't aware of this -- I caught the reference as soon as I heard the commercials, but everyone around me was saying "Why is Shatner trying to sing those songs? He's terrible!" Ah, but that was the point...
"Leopard-Skin Pillbox Hat"
"Visions of Johanna"
"Positively 4th Street"
"Stuck Inside of Mobile With those Memphis Blues Again"
"It's Alright Ma"
"Lay Lady Lay"
"Ballad of a Thin Man"
"Just Like a Woman"