Some songs are great and are widely considered great. Stairway to Heaven, Bohemiam Rhapsody, and so on. Some songs aren't considered great by the population as a whole, but earn their due respect from their audience. A Change of Seasons, 2112 by Rush, and so on.
Some songs unfortunately are great but aren't widely respected. This thread is for those songs.
My addition:
Linkin Park - Session
I'm not sure how much of a secret this song is, but its respect level is out of proportion to its quality. I've never heard another song even remotely like it, even by Linkin Park. The drums combine both granular synthesis/stutter beats and booming size, which should be impossible. The synth tones are dark and moody, without being over emotional relative to the purpose of the song. And that scratch solo. Awesome. It's a shame DJ Hahn doesn't do much DJing in Linkin Park anymore, because he was awesome.
This song isn't one of the greatest ever, but it basically came and went from the public consciousness, which isn't fair.