Go to youtube, and enter “Clarinet and organ” into their search box – it's surprising how many items appear. There's also quite a lot for saxophone and organ.
I'm fond of Finzi's Five Bagatelles for clarinet and piano; the Romance is really beautiful, and works as an organ solo; so it should also work if you can see how to transcribe the piano part for organ:
http://www.youtube.com/watch?v=EN3a18rEB_8The organ actually sounds well with most instruments – I wish people would be more enterprising about exploring the possibilities. A friend of mine arranged Walford Davies' “Solemn Melody” for organ and recorder ensemble, so that his school recorder group could play it while processing – it sounded wonderful! One of my pupils is a good violinist, so we arranged John Ireland's Vilanella for violin and organ – it was fine. Instead of alternating the melody between manuals, alternate between organ and violin. This performance is possibly a little fast, but will give you an idea:
http://www.youtube.com/watch?v=K8z3B286TsoYou could also try the Bach trio sonatas - just transpose one of the lines for clarinet.
Good luck!