So, I’ve been watching “Once More, With Feeling!” too much lately, and I found myself wondering, other than “Rest In Peace”, what are some good rock songs involving pipe organs?
“A Whiter Shade of Pale” by Procol Harum.
Iron Butterfly has some serious church-sounding, non-church organ stylin’ of a non-pipe nature. So, honestly, it has nothing to do with this thread. Forget I mentioned it (“Inna Gada da Vida”, anyone?).
OK, and that’s really the only song of theirs I can name.
Deep Purple’s Lazy.
“Journey to the Center of the Earth” by Rick Wakeman might be good for you.
Look into Rick Wakeman for other examples.
Just pipe organs, or the organ in general? 'Cuz The Doors has the organ-as-integral-part-of-the-band category pretty nearly wrapped up, unless of course you happen to think of Emerson, Lake and Palmer or Yes, but that’s also a lot of other keyboards as well.
How 'bout “In-A-Gadda-Da-Vida,” then?
Oooh, creamy simulpost goodness! 
There’s a Hammond organ on nearly every Allman Brothers Band song ever recorded.
John Fogerty’s “Centerfield” uses a Hammond to give it a ballpark feel.
Eli’s Coming by Three Dog Night is pretty nice.
Genesis. The beginning of Watcher of the Skies is all organ.
The lone album by one of Billy Joel’s early groups, Atilla, features probably the only organ and drums duo in rock history. One listen and you’ll see why there haven’t been any organ and drums duos since.
Damn near anything by the Purps, with Jon Lord vs Ritchie Blackmore organ/guitar duels.
Well, not sure if this counts, since it’s only an intro, but the first half-minute or so of George Michael’s “Faith” is with pipe organ.
Burn is my Deep Purple organ filled fav.
There’s X2, although I think they’re more in the funk/jazz vein. From what I’ve heard, Atilla tried to do something like metal.
I know Led Zeppelin had a few in there, but the only one that comes to mind off the top of my head is “Your Time is Gonna Come”
The studio version of Free Bird has an organ/keyboard bit. This is the version most often used by the Free Birds (Hayes, Gordy, and Roberts) for their ring entrance. Worked very well with the “Free Bird Strut”…
Lee Michaels (Do you know what I mean?)
The Rolling Stones’ “I Got The Blues” has a brilliant organ riff. Was it Billy Preston playing that?