I did YGMCB last year at a 450 seat theatre and the royalties for the new version were $975 per performance. I don't know if they would be that much for a much smaller theatre, but they are definitly more expensive than most shows. I had a great time doing it though!
I really enjoy Michael John LaChiusa's small one act musicals... Break, Lucky Nurse, Eulogy for Mr. Hamm, and Agnes. They are fresh, different stories and something new. I also love his First Lady Suite which has only 7 people in it (6 women, 1 man).
I also like Wings (the musical), A Man of No Importance, Ruthless, The Spitfire Grill, and They're Playing Our Song.
From the evil she done Lord
Set her free, Set her free, Set me free
Don't let my sorrow
Make evil of me