The preferred way to cite Avogadro is:

  • Avogadro: an open-source molecular builder and visualization tool. Version 1.XX.
  • Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison; “Avogadro: An advanced semantic chemical editor, visualization, and analysis platform” Journal of Cheminformatics 2012, 4:17.

Please make sure to cite the particular version of Avogadro you use.