I was listening to “What It Takes” by Aerosmith. It’s a great song, and has an accordion in it.
Then the other day I heard Paul Simon;s “Boy in the Bubble.” Also great, also with an accordion. (Or a synthesizer that sounds like an accordion. Same thing.)
Any other examples?
I don’t know what you consider great rock/pop. Most of They Might Be Giants’ catalog has accordion. I think a lot of it is great.
The Stones’ “Backstreet Girl” (Brian Jones on accordion).
Back to the beginning.
Rock Around the Clock. Bill Haley and the Comets featured an accordion.
Jethro Tull: “Queen and Country”
Emerson, Lake & Palmer: “C’est la Vie”
“Stereo Love” is a recent dance song with one.
Bugs by Pearl jam
“My Bologna” by “Weird Al” Yankovic
What?
The Bonzo Dog Band’s “The Intro and the Outro” has General DeGaulle on accordion as part of their all-star session musicians. 
Don’t forget “My Pink Half of the Drainpipe.”
Arcade Fire
I think the Band used an accordion from time to time. “When I Paint my Masterpiece” seems to have it.
How Can I Be Sure, Young Rascals
Squeeze Box by The Who, of course. (Though, oddly, the accordion isn’t exactly front and center in the mix.)
“Sweethearts Together” by the Stones, and “Streets of Bakersfield”, a country rocker by Dwight Yokum and Buck Owens. Both feature conjunto accordianist Flaco Jiminez.
Not sure how the original recording was orchestrated, but when The Band reassembled for Dylan’s 30th anniversary bash they used two accordians on Masterpiece. For the life of me, I can’t remember who was playing them.
SS
R.E.M. 's “I Believe” isn’t bad.
Pull Up to the Bumper
Grace Jones
The Beatles’ “We Can Work It Out”
Dave Edmunds’ “Bail You Out”
John Cougar Mellencamp’s “Check It Out”
The Young Rascals’ “How Can I Be Sure?”
The Hooters’ “Karla With a K”
Billy Joel’s “Scenes from an Italian Restaurant”
The song is not everyone’s cup of tea, but Springsteen’s Sandy (4th of July) has great accordion by the late Danny Federici.
And more recentlly, to great effect on “Oh My Heart.”
