Citation
From Avogadro - Free cross-platform molecule editor
At the moment, there is no publication describing Avogadro, although one is in the draft stages.
The preferred way to cite Avogadro is:
Avogadro: an open-source molecular builder and visualization tool. Version 1.XX. http://avogadro.openmolecules.net/
Please make sure to cite the particular version of Avogadro you use.