After more than two decades of making numerous shorts, providing animated segments for documentaries such as Blue Vinyl and the musical feature Hedwig and the Angry Inch, Hubley made her first feature, The Toe Tactic. The Toe Tactic had its theatrical premiere at the Museum of Modern Art in January 2009 and was released on DVD by Kino International. The cast includes Lily Rabe, Daniel London, Kevin Corrigan, Sakina Jaffrey, Novella Nelson, Mary Kay Place and Jane Lynch. Extensive voiceovers for the animated characters were provided by Eli Wallach, Marian Seldes, Andrea Martin, jazz musician Don Byron and comedian David Cross, The music was written and performed by Yo La Tengo. Her hand-drawn films explore personal memory and the turbulence of emotional life. Among Hubley's shorts are Octave, Pigeon Within, Her Grandmother's Gift (in collaboration with her mother Faith), The Tower (in collaboration with her sister Georgia), and Delivery Man. In 2010, she completed a series of animated pieces for Motherhood: Out Loud, a new play presented at Hartford Stage in February — March 2010. Other animated sequences were provided by Hubley and Jeremiah Dickey to the documentary Everything’s Cool by Judith Helfand & Dan Gold, and The Boy In The Bubble by Barak Goodman & John Maggio. Her company, Hubbub Inc, also created short form series for the cable networks Nickelodeon and Lifetime.
Other projects have included work for Disturbing the Universe: Radical Lawyer William Kunstler directed by Emily and Sarah Kunstler and What's On Your Plate? directed by Catherine Gund. A daughter of pioneer animators Faith and John Hubley, Emily worked on Faith Hubley's films at The Hubley Studio, Inc. from 1977 to 2001.