While appearing on the series, the actor branched out into film work, appearing in Steven Spielberg's "1941" in 1979 and the similarly military-themed comedy "Stripes" in 1981. A role in the zany "Going Berserk" (1983) teamed him up with fellow Second City performers John Candy and Eugene Levy, while a role as the aptly named Sid Sleaze in the children's feature "Sesame Street Presents: Follow That Bird" introduced him to a younger audience. The tall, slim and versatile actor made a somewhat imposing figure, an image he either underscored with portrayals of hardheaded villains and exasperated authority figures or played against as dim, ineffectual goons. Racking up credits in the 1986 features "One Crazy Summer" and "Club Paradise", Flaherty proved a character actor who would survive the demise of "SCTV". That year he returned to television as the writer, host and executive producer of the HBO anthology "Really Weird Tales", a spoof of suspense programs. When fellow "SCTV" veteran Martin Short landed his own animated series "The Completely Mental Misadventures of Ed Grimley" (NBC, 1988-89) Flaherty provided some live-action performances, reprising his popular Count Floyd character. His performance in the 1989 Disney Channel movie "Looking For Miracles" earned him a Gemini, the Canadian equivalent of an Emmy. That same year he appeared in an episode of "Married... With Children" (Fox) as a loony dentist, and had similarly scene-stealing supporting roles in the features "Who's Harry Crumb?", "Speed Zone" and "Back to the Future II".

1990 marked Flaherty's successful return to regular series television, playing wacky inventor Fred Edison on the Family Channel series "Maniac Mansion". The series helped the network live up to its name throughout its three-season run (which repeated for an additional two seasons), entertaining children with it's wacky science and keeping parents happy thanks mostly to Flaherty's affectionate take on the eccentric inventor. Here the actor/writer/producer added director to his many titles, helming episodes of the popular sitcom. His guest appearances on 1994 episodes of the forgettable series "Hardball" (Fox), "Phenom" (ABC) and "Nurses" (NBC) were arguably the brightest spots in the sitcoms' dark future, while his portrayal of a father of a missing girl in the Showtime remake "Runaway Daughters" showed impressive range. In 1995, he was featured in two dysfunctional family-themed comedy projects, ABC's "Family Reunion: A Relative Nightmare" and the "Saturday Night Live" spin-off feature film "Stuart Saves His Family". A 1996 guest spot on "Ellen" (ABC), a supporting role in the hit comedy feature "Happy Gilmore" and a regular role on the short-lived syndicated sitcom "Police Academy: The Series" (1997) kept the actor in the public eye, as did his role as the titular psychiatrist in The Movie Channel-premiered comedy "The Don's Analyst" and a part as the dogcatcher in the ABC comedy TV-movie "Dogmatic".

A 1996 recurring role on the CBS series "The Louie Show" introduced the actor to up and comer Paul Feig, an actor-producer who would later cast the admired veteran on his own series, the critically-acclaimed ratings loser "Freaks and Geeks" (NBC). The 1980-set series was a heartbreakingly realistic take on the American high school experience, and Flaherty added enjoyable comic relief as Harold Weir, an overbearing father of freak Lindsey and geek Sam, who employed prophet of doom parenting tactics in an effort to scare his remarkably well-adjusted children into behaving. As with many of Flaherty's portrayals, Harold's seemingly two-dimensional wackiness was fortified by sympathetic, human underpinnings that the actor evinced through subtle and unexpected peeks below the surface. Winning even more fans through this portrayal, Flaherty was missed on the small screen, and when he returned for the 2001 NBC summer series "Go Fish", viewers were happy to see the bizarre dad on their sets again. That same year he lensed the adventure comedy "National Security", directed by Dennis Dugan.