Shawn has appeared in over 70 movies and 30 TV shows (see IMDb) so I've only included the more major roles.
The Mandrake (1977), by Niccolo Machiavelli, translated and adapted by Shawn.
The Hotel Play (1981), by Shawn, directed by John Ferraro: As The Hate-Filled Husband.
Aunt Dan and Lemon (1985), by Shawn, directed by Max Stafford-Clark: As Lemon's Father, Freddie, and Jasper.
The Fever (1990-99), by Shawn: Solo performances in various venues.
Uncle Vanya (1990-94), by Anton Chekhov, adapted by David Mamet, directed by Andre Gregory: As Vanya. Not a full production but an ongoing workshop led by Gregory over a span of years, with rehearsals attended by small invited audiences in a closed Times Square theater. Louis Malle filmed their work as Vanya on 42nd Street.
Wifey (1994), written and directed by Tom Noonan: As Cosmo, a role that Noonan wrote for him. Noonan got an Obie Award, and soon directed a film version with the same cast (retitled The Wife) which was well reviewed but not widely seen. The play is a four-character pressure-cooker of marital dissatisfaction, whose themes and tone owe a great deal to Shawn though the writing is more naturalistic.
The Designated Mourner (2000), by Shawn, directed by Andre Gregory: As Jack. (Also produced for radio in 2002.)
Manhattan (1979), written and directed by Woody Allen: As Jeremiah, Shawn's first film role, due to Allen having seen his stage debut in The Mandrake. Jeremiah, the ex-husband of Isaac's (Allen's) girlfriend Mary (Diane Keaton), is described by Mary as a sexual dynamo and by Isaac as a "little homunculus."
My Dinner with Andre (1981), written by Shawn and Andre Gregory, directed by Louis Malle.
Radio Days (1987), written and directed by Woody Allen: As The Masked Avenger.
The Princess Bride (1987), written by William Goldman, directed by Rob Reiner: As Vizzini, the tightly-wound evil genius to whom anything unexpected is "inconceivable!"; his excessive trust in his intelligence proves fatal.
The Moderns (1988), written by Alan Rudolph and John Bradshaw, directed by Rudolph: As Oiseau, a gossip columnist in 1920s Paris.
Vanya on 42nd Street (1994): See Uncle Vanya in Stage.
Clueless (1995), written and directed by Amy Heckerling, based on Emma by Jane Austen: As Alphonse Hall, a Beverly Hills high-school teacher. Kept the same role in the spin-off TV series from 1996-97.
The Wife (1995), written and directed by Tom Noonan: See Wifey in Stage.
Toy Story (1995): As Rex, a nervous plastic dinosaur.
Toy Story 2 (1999): Rex again.
The Incredibles (2004): Mr. Incredible's tiny, querulous boss, Mr. Huph.
Taxi (1978): As Arnie Ross in two episodes, his first TV appearance, helping to guarantee his constant employment as short bald comic relief.
The Cosby Show (1987-1991): As Jeff Engels.
Star Trek: Deep Space Nine (1993-1999): As Grand Nagus Zek, which may now be Shawn's best-known role next to Vizzini. The Nagus was the leader of the Ferengi, an alien species who were short, bald, huge-eared, nervous, and obsessed with money—which many viewers took as a Jewish stereotype, but might more specifically describe a caricature of Shawn himself.
Murphy Brown (1994-1997): As Stuart Best.
Crossing Jordan (2001-2003): As Dr. Howard Stiles.
Radio production of The Designated Mourner (2002), by Shawn, directed by Andre Gregory: As Jack.
Voiceover performance in A.M. Hoch's multimedia installation Mitosis (2003), text by Hoch, also featuring Deborah Eisenberg.