The only one i recall matching up like the book was All along the Watchtower.
I really wanted to hear that Iggy Pop song 'Neighbourhood Threat' which plays through the knottop's ghettoblaster when Dan is walking home the first time.
there was a Billy holiday one 'You're my thrill' that pplayed in the owl ship i thought they would use too.
some people have complained that the songs were too famous, and maybe obvious, but i read someone on a message board saying that they had to be famous songs, to go along with the fact that we were watching an alternate history, songs that marked the time in which they were written, Boogie Man for the 70s, Sounds of silence being a famous 60s song(i know they did not play it in the 60s setting, but still), 99 Red Balloons for the 80s...
Boogie man/riot scene is one of my fav superhero movie moments ever, the first time i saw it i was a bit wtf?! it is not the kind of tune you imagined playing over that scene when you read the book, as it was a bit grim, but it kind of makes it funny in the movie, the Comedian kicking the crap out of people to disco music.
The opening was amazing too with the Dylan song as you say, I sometimes sit and think, 'holy moses, if they had taken the money they used to film all of those scenes for the credits, they could have filmed more of the book!', lol, it is amazing how much trouble they went to for the opening credits.
Sometimes when watching the movie I will skip the credits though, as I like the effect of seeing the yellow smiley badge being panned down on and then zoomed right back from, which you can just catch if you time your dvd ff button just right.