Even the cleanest coop is going to smell sometimes because chickens make incredibly nasty smelling cecal poop. I like Strong Animals' Coop Recuperate, which includes essential oils and comes in seasonal scents -- for my enjoyment, not the chickens'.
For example, last fall Strong sold an orange, cinnamon and clove limited edition, and the container even has a scratch-and-sniff patch so you can try out the fragrance at the store. I buy mine at the local Bomgaars farm store (which is only a Midwest chain, but I think it's readily available elsewhere).
Just shake it on top of the litter in the coop, and enjoy the improved aroma.