In the late 1990s, he embraced work in independent film, appearing in a number of roles. Several of his independent films have won awards: The Good Things, in which Wheaton portrays a frustrated Kansas tollbooth worker, was selected Best Short Film at the 2002 Deauville Film Festival. He also received the Best Actor award at the 2002 Melbourne Underground Film Festival for his performance in Jane White is Sick and Twisted. He was also a contestant on a Star Trek-themed episode of The Weakest Link, and performs improvisational and sketch comedy at the ACME Comedy Theater in Hollywood. He has a travelling sketch comedy/improv troupe called "EarnestBorg9" that performs Sci-Fi and geek-related comedy at conventions.

Although his character (and by extension Wil himself) was loudly hated by a small but vocal group of Trekkers (see Usenet group alt.ensign.wesley.die.die.die or alt.wesley.crusher.die.die.die) during TNG's first run, Wheaton has emerged as a vocal member of the geek / nerd community and runs his own weblog, Wil Wheaton Dot Net. The majority of his present popularity comes from this web site, the books it has spawned, and from fans who admire his earlier work. He is a frequent poster at Digg, Slashdot and Fark, and is heavily involved with the Electronic Frontier Foundation, promoting free speech and privacy issues. Wil also contributes regularly to the Los Angeles-based Metroblogging site. His work as a voice actor can be found in such diverse places as Aqualad of the cartoon Teen Titans and, most recently, as the voice of radio newsman Richard Burns in the popular Grand Theft Auto: San Andreas video game.

Wheaton married Anne Prince in 1999. He lives with his wife and two step-sons in Los Angeles, California. Wheaton is often confused with Will Wheaton Jr., a jazz musician who contributed to the film Mystery Men, among other works.

In the spring of 2003, Wheaton founded the independent publishing company Monolith Press and released a book of his memoirs, entitled Dancing Barefoot. "Monolith Press was founded on the idea that publication should not be limited by opportunity." At the time of this writing, the only book published is Dancing Barefoot. Most of the entries are extended versions of his online blog entries. Wheaton sold out three printings in four months, and in the winter of 2003, the book's success caught the eye of publisher Tim O'Reilly, who signed Wheaton to a three book contract. O'Reilly acquired Dancing Barefoot, and published Wheaton's extended memoirs, Just A Geek, in summer of 2004.

Wil had a monthly column entitled "Wil Save" in the Dungeons and Dragons based magazine Dungeon, where he related anecdotal tales of his life in relation to the famous fantasy RPG. He ceased writing the column in May 2005. In January 2005, Wil began a column about video games in The Onion and in June 2005 became the feature Geek editor for the SuicideGirls Newswire.

In February 2005, Wil announced that he had won the role of a one-off character, the crack-addicted homeless man Walter, on CSI (Episode #5.17: "Compulsion" March 10, 2005). A March 10 New York Times column by John Schwartz portrayed Wil's role in a highly favorable light. Duane Clark, director of the episode, is quoted as saying " a lot of scary volatility . He really dug his teeth into it, and on his own came up with a backstory of who Walter was. He really filled out what could have been a caricature."

In 2003, Wheaton began noting on his blog his love for the game of poker. The following year, Wheaton began writing more extensively about his poker-playing experiences, including stories about playing Texas hold 'em tournaments locally and in Las Vegas. Eventually, Wheaton worked up to regular play, including a notable run at the 2005 World Poker Tour Championships. On June 23, 2005, Wil accepted an invitation to join Team PokerStars . He went on to play in that year's World Series of Poker.

As of April 2006, Wil has been signed on to the new Nickelodeon cartoon, kyle + rosemary, as the titular Kyle.