I don't know if I would call these the greatest rock songs but they're definitely must listens for old and new indie/rock listeners.
Arcade Fire - Tunnels + Wake Up
AFI - But Home Is Nowhere
The Beatles - A Day In The Life
Billy Idol - White Wedding
David Bowie - Heroes
Faith No More - Epic + Out of Nowhere
Guns 'n' Roses - November Rain
Joy Division - Love Will Tear Us Apart
Led Zeppelin - Stairway to Heaven
Marilyn Manson - Coma White
Meat Loaf - Bat Out of Hell
Neil Young - Hey Hey, My My (Into the Black)
Nightwish - Nemo
Nine Inch Nails - Hurt
Radiohead - Paranoid Android
Rolling Stones - Gimme Shelter + Sympathy for the Devil
The Cure - Lovesong
The Police - Message in a Bottle
The Verve - Bittersweet Symphony