Songs that use a church organ?

Hammond organs were a staple of rock in the 50s and 60s. There are too many examples to list here; Ray Manzarek's output alone is extensive. A web search for "hammond organ rock" will get you scads of examples.

True church organs (i.e., pipe organs) have been used more rarely, but this wiki should get you to some of them.

http://en.wikipedia.org/wiki/Organ_%28music%29#Roc...

Puzzlin' Evidence, Talking Heads!

Well, try The Organ:

Memorize The City

http://www.youtube.com/watch?v=GOUAOAgThaw

Love, Love, Love

http://www.youtube.com/watch?v=h8trKYzgQF0

Brother

http://www.youtube.com/watch?v=5GdgEXaF2sk

Funeral for a Friend, by Elton John on the Goodbye Yellow Brick Road album.

Your Time Is Gonna Come by Led Zeppelin

The intro part^^^

All Black by Good Charlotte

http://ultimateclassicrock.com/organ-rock-songs/

http://www.classicrockforums.com/forum/f49/my-top-...

Inagodadavida

"Rain" by Yoko Kanno, from the Cowboy Bebop soundtrack.

Where will you go by Evanescence

http://www.youtube.com/watch?v=YSdaagf6MZQ