Weller followed up his success in "Naked Lunch" with several lackluster projects: the action adventure "Fifty-Fifty" (1991); a French romantic comedy "Road To Ruin" (1992); and the thriller "Sunset Grill" (1993), all of which moved quickly to home video. Career matters started looking up with the release of Michael Tolkin's "The New Age" (1994), where he was paired once again with "Naked Lunch" co-star Judy Davis. Weller got to demonstrate his flair for comedy playing a jobless Hollywood ad man whose marriage is crumbling. Although the film and Weller both received rave reviews, the actor's profile dimmed through the late 1990s; while he worked steadily, only a few films stood out, such as Woody Allen's "Mighty Aphrodite" (1995) and director Linda Yellen's "End of Summer" (1996). He resurfaced in the admired Showtime science fiction series "Odyssey 5" (2002-2003) playing Chuck Taggert, part of a team of space shuttle astronauts who witness the end of the world and travel back in time to prevent the disaster from occurring. Weller was seen on the big screen again in 2003, playing Cardinal Driscoll, a high-ranking church official given to ungodly actions in the secret sect thriller "The Order."

Weller has also stepped behind the camera as a director, helming episodes of "Homicide: Life on the Streets" and "Odyssey 5" and the telepics "Partners" (1993) and Elmore Leonard's "Gold Coast" (1997). But for the most part, Weller stuck to acting. After a brief hiatus from feature films, he returned to the big screen in 2000 with a vengeance. In “Shadow Hours,” he played a shady character claiming to be a writer who convinces a gas station attendant (Balthazar Getty) to join him on a journey through the hellish and depraved world of underground S&M clubs and pit fitting in Los Angeles. After playing a megastar landed by Hollywood’s über-talent agent (Danny Huston) in “Ivan’sXTC,” a modern take on Leo Tolstoy’s Death of Ivan Illyich, he played a State Department official in Paris in “Falling Through.”

Weller then played an innocent security inadvertently carrying a lethal toxin in the Cinemax thriller, “Contaminated Man” (2000). After appearing in the straight-to-video thriller, “Styx” (2001), about an ex-robber dragged into One Last Heist by his gambling-addicted brother, Weller popped up for the last five minutes as a hotshot record producer in “Undiscovered” (2005), an insipid romantic drama about fame-hungry singers guided by random fate and superficial ambitions. The “Glitter”-wannabe remained true to its name by failing to crack seven figures in wide release opening weekend.