One thing that puzzles me -- and some of the responses to this thread continue the confusion -- is why every song done by a "rock band" gets labelled "rock," even if it's a slow ballad (e.g., Ruby Tuesday, Yesterday, Michelle, or Here There & Everywhere, or a slow, bluesy song like the slow version of Layla. IMNSHO opinion, many "rock" bands and artists are ecelectic enough that their music runs from rock to reggae to blues to ballads to country and even semi-classical.
In that vein, I'd nominate Ray Charles's "What'd I Say?" as one of the greatest rock songs of all time, but many of his other great hits weren't even close to being "rock ('n' roll)."

Some of my other nominees include:
Long Cool Woman In A Black Dress - The Hollies
Louie, Louie - The Kingsmen
To quote PoppaGator:
"...Louie Louie" has an interesting history, and an album was once made (around the end of the vinyl era) composed of nothing but versions of this one song. ...
The Kingsmen's hit was the third recording; they learned it from listening to version #2 on jukeboxes and local radio in Seattle. Since the singer himself couldn't decipher the words, he is actually faking it, scatting non-verbal "lyrics" in places -- hence the reaction that whatever he was saying *must* be nasty. ..."
LOL! :-D

That song, I think, counts as "folk" if only because it's become so well-known to school kids and every garage band everywhere that rock bands are refusing to play it any more. Others in this category are:
Stairway To Heaven - Led Zeppelin
To quote John P:
"The most over-played song in history is probably "Stairway to Heaven" by Led Zeppelin. The thing is, there's a reason it's been over-played. It's a bloody great rock song."

and
Born To Be Wild - Steppenwolf
Satisfaction - The Rolling Stones


Other nominees:
Brown Sugar - Rolling Stones
Pretty Womab - Roy Orbison
We Will Rock You - Queen
Great Balls Of Fire - Jerry Lee Lewis
Johnny B. Goode - Chuck Berry
Sultans Of Swing (or Money For Nothing) - Dire Straits
Bye, Bye, Love - Everly Brothers
Not Fade Away - Buddy Holly (later covered by The Grateful Dead)
Bad Moon Rising - CCR