I think emotion has a lot to do with it. I heard "Confidence Man" by Jeff Healey on the radio the other day and it gave me goosebumps. That song has never had that effect on me before, so it's obviously something to do with his recent death that was causing the reaction.
I agree with Shine On You Crazy Diamond being a really emotive song. That again, being about Syd Barrat, triggers the emotion senses plus the atmosphere of the production on that record is amazing.
The number one song that really gets me emotional every time I hear it is Green Day and Wake Me Up When September Ends. It was in the charts, and played constantly, around the time I had to have my pet cat Biscuit put down. I can remember driving home from work the day after we'd been to the vets and crying my eyes out for the length of the track. My eyes are welling up now as I type this!
A very powerful thing, music and emotions...