In addition to being a regular on three TV shows in three different genres (Benson (situation comedy); Star Trek: Deep Space Nine (science fiction); and Boston Legal (legal drama)), Auberjonois has been a guest star on many different television series, including The Rockford Files, Charlie's Angels, The Jeffersons, The Outer Limits, Night Gallery, Matlock, Murder She Wrote, Frasier, Judging Amy, Chicago Hope, Star Trek: Enterprise, Stargate SG-1, The Practice (for which he received another Emmy nomination, playing a different character than the one he has played on The Practice spinoff Boston Legal), and Saving Grace. Television movie credits include Disney's Geppetto, Gore Vidal's The Kid, the remake of the classic, A Connecticut Yankee in King Arthur's Court, and the miniseries Sallie Hemings: An American Scandal (2000). He received a third Emmy Award nomination for his performance in ABC's The Legend of Sleepy Hollow.

Auberjonois has voiced several roles, including characters on Snorks, Batman: The Animated Series, Avatar the Last Airbender, Xiaolin Showdown, Justice League Unlimited, and Max Steel.

Auberjonois has directed some TV shows, including Marblehead Manor and several episodes of Deep Space Nine.

After M*A*S*H, Auberjonois's movie roles have included the gangster Tony in Police Academy 5: Assignment Miami Beach (1988) and Reverend Oliver in The Patriot (2000, starring Mel Gibson). He has had some rather exotic cameos in a number of films, including Dr. Burton, a mental asylum doctor patterned after Tim Burton, in Batman Forever, and a bird expert who gradually transforms into a bird in Robert Altman's 1970 film Brewster McCloud. He cameod as Colonel West in the 1991 Star Trek film Star Trek VI: The Undiscovered Country. Other notable film appearances have included McCabe & Mrs. Miller (1971, starring Warren Beatty), The Hindenburg (1975, co-starring George C. Scott), the first remake of King Kong (1976), The Big Bus (1976), Eyes of Laura Mars (1978), Where The Buffalo Roam (1980), Eulogy, The Feud, and Inspector Gadget (1999). Auberjonois also portrayed the character of Straight Hollander in the 1993 Miramax film The Ballad of Little Jo. In 2004 he did the voice for "Bio-Constrictor" for the Direct-to-DVD movie Max Steel: Endangered Species. He voiced Chef Louis in the 1st and 2nd Little Mermaid films and the Butler in Joseph: King of Dreams.

Auberjonois has also been active in radio drama. Among other programs, he read "The Stunt" by Mordechai Strigler for the NPR series Jewish Stories From the Old World to the New. He has also recorded a number of novels on tape. As for film voice-overs, he was heard in Disney's The Little Mermaid (receiving top billing as Chef Louis), and as The Skull in The Last Unicorn. He reprised an animated version of his character Odo from Star Trek: Deep Space Nine in a cutaway dzoke in Family Guy's Stewie Griffin: The Untold Story. The cutaway featured Odo threatening Stewie's alleged cousin Quark Griffin.

He also did the voice of Vanity Smurf from the Smurfs series in the 1980s, Dr. Braxis in Challenge of the GoBots, and was the voice of Peter Parker on the 1972 Buddah Records Spider-Man LP "From Beyond the Grave" (BDS 5119), a radio-style narrative replete with sound effects and rock and roll song interludes provided by "The Webspinners", in which the characters of The Vulture, The Lizard, The Green Goblin, The Kingpin and Dr. Strange also appeared. In 1984 and 1985, Rene gave voice to Desaad, an associate of the villainous Darkseid on the animated series, Superfriends. Rene also provided the voice for Janos Audron, an ancient vampire in the Legacy of Kain video game series; he was in Soul Reaver 2, Blood Omen 2, and Legacy of Kain: Defiance. He also provided the voice of Angler in the Pirates of the Caribbean: At World's End video game. He voice-played General Zod in the Joseph Ruby-Kenneth Spears animated Superman series episode titled "The Hunter".