In 1999, Baker established a non-profit corporation, the American Newspaper Repository, to rescue old newspapers from destruction by libraries. In 2001 he published Double Fold, in which he accuses certain librarians of lying about the decay of materials and being obsessed with technological fads, at the expense of both the public and historical preservation.
Baker describes himself as having "always had pacifist leanings."
In March 2008, Baker reviewed John Broughton's Wikipedia: The Missing Manual in the New York Review of Books. In the review, Baker described Wikipedia's beginnings, its culture, and his own editing activities under the username "Wageless". His article "How I fell in love with Wikipedia" was published in The Guardian newspaper in the UK on April 10, 2008.
U and I: A True Story (1991) is a non-fiction study of how a reader engages with an author's work: partly an appreciation of John Updike, and partly a kind of self-exploration. Rather than giving a traditional literary analysis, Baker begins the book by stating that he will read no more Updike than he already has up to that point. All of the Updike quotations used are presented as coming from memory alone, and many are inaccurate, with correct versions and Baker's (later) commentary on the inaccuracy given in brackets.
Vox (1992) consists of an episode of phone sex between two young single people on a pay-per-minute chat line. The sex scenes in the novel, though quite vivid, nevertheless share the basic approach that Baker has taken since The Mezzanine: in this case, he explores two characters' accumulated thoughts and memories in relation to sex. For some readers, Baker's obsession with detail detracted from a hoped-for pornographic effect. Others, in reading the imaginative sex stories the two protagonists produce for one another, have perceived a budding romantic affection: in the last act they perform before hanging up, the man gives the woman his phone number. The book was Baker's first New York Times bestseller. Monica Lewinsky supposedly once gave a copy to President Bill Clinton.
The Fermata (1994) also addresses erotic life and fantasy. To quote the dust jacket of one edition: "Arno Strine likes to stop time and take women's clothes off. He is hard at work on his autobiography, 'The Fermata.' It proves in the telling to be a very provocative, funny, and altogether morally confused piece of work." (A fermata is a mark in musical notation indicating a note should be sustained.)
The Everlasting Story of Nory (1998) was inspired by Baker's daughter Alice, "the informant", to whom he dedicates the book. In this work, Baker tries to see the world through the eyes of a curious nine-year-old American girl attending school in England.
Double Fold: Libraries and the Assault on Paper (2001) is a non-fiction book about preservation, newspapers, and the American library system. An excerpt first appeared in the July 24, 2000, issue of The New Yorker, under the title "Deadline: The Author's Desperate Bid to Save America's Past." The exhaustively researched work (there are 63 pages of endnotes and 18 pages of references in the paperback edition) details Baker's quest to uncover the fate of thousands of books and newspapers that were replaced and often destroyed during the microfilming boom of the 1980s and 1990s.
A Box of Matches (2003) is in many ways a continuation of Room Temperature, similarly mining the narrator's store of reflections and memories, many of them domestic. The narrator is now middle-aged and has a family. He rises each morning about 4:00, lights a fire in the fireplace, and ponders. The work is admired, although some have found it rather less exuberant than its predecessor.
Checkpoint (2004) is composed of dialogue between two old high school friends, Jay and Ben, who discuss Jay's plans to assassinate President George W. Bush. Jay is an unbalanced day laborer who, in the depths of his anger and desperation at Bush's actions and his inability to do anything to stop them, has traveled to Washington, D.C., to kill the president. He considers many far-fetched means of assassination, such as depleted uranium boulders, flying radio-controlled CD saws, homing bullets trained to target the victim by being "marinated" in a tin with a picture of the president, and hypnotized Manchurian scorpions. Ben has met Jay in a Washington, D.C., hotel room, unaware that his friend is planning to commit "a major, major, major crime." Over the course of the novella, Ben discusses what drove Jay to plot an assassination. Reviewers have pointed out that the book is mild, and the planned violence so cartoonish as to be non-threatening.
Human Smoke: The Beginnings of World War II, the End of Civilization (2008) is a history of World War II that questions the commonly held belief that the Allies wanted to avoid the war at all costs but were forced into action by Hitler's unforgiving crusade. It consists largely of official government transcripts and other documents from the time. In form it is similar to Sven Lindqvist's "A History of Bombing" (New York: New Press, 2001), which Baker includes in the book's copious list of references. Baker cites documents that suggest that the leaders of the United States and the United Kingdom were provoking Germany into war (showing, for example, that Britain bombed Germany before Germany bombed Britain) and that the leaders of those two nations had ulterior motives for wanting to participate. In the epilogue to the book he suggests that the pacifists (who are often vilified by World War II historians) had it right all along, stating: "They failed, but they were right."  Some reviewers savaged Human Smoke, the historian Noel Malcolm describing it as a "strangely childish book" and William Grimes as a "self-important, hand-wringing, moral mess of a book" that was "muddled and often infuriating". Author Christopher Hitchens accused Baker of ahistoricism and wrote that the book served as a reminder of how "fatuous the pacifist position can sound, or indeed can be". Conservative political commentator R. Emmett Tyrrell, Jr. awarded his J. Gordon Coogler Award for Worst Book of 2008 to Human Smoke. Other reviewers praised Baker's use of documentary research and the intricate construction of the text. Colm Toibin wrote in his New York Times review that "the issues Baker wishes to raise, and the stark system he has used to dramatize his point, make his book a serious and conscientious contribution to the debate about pacifism," and Mark Kurlansky wrote for the Los Angeles Times that "People are going to get really angry at Baker for criticizing their favorite war. But he hasn't fashioned his tale from gossip. It is documented, with copious notes and attributions. The grace of these well-ordered snapshots is that there is no diatribe; you are left to put things together yourself. [Human Smoke] may be one of the most important books you will ever read."
The Anthologist (2009) is narrated by Paul Chowder, a poet, who is attempting to write an introduction to a poetry anthology. Distracted by problems in his life—Chowder's career is going nowhere, and his girlfriend has recently left him—he is unable to begin writing, and instead ruminates on poets and poetry throughout history.
House of Holes (2011) is a collection of stories, more or less connected to each other. The novellas are erotic in the sense of Giovanni Boccaccio's Decameron. The titular House of Holes is a fantasy sex resort in which people can engage in absurd sexual practices, such as groin transference and sex with trees. Akin to Alice, people enter the House of Holes through such techniques as tumbling through a clothes dryer or through a drinking straw. It is a book of romantic fairy tales subtitled "A Book of Raunch".
Traveling Sprinkler (2013) brings back Paul Chowder from The Anthologist. Having finished his anthology of verse poetry, Chowder is trying to write his own lyric poems, but seems to only produce lyrics. He decides to concentrate on making songs, buying software and instruments that allow him to record complex dance music tracks. He remembers his days playing bassoon, and considers its place in classical music. He continues his relationship with his ex-girlfriend, and muses on cigars, drone warfare, traveling sprinklers, and more.
Cox, Richard J. Vandals in the Stacks? A Response to Nicholson Baker's Assault on Libraries. Greenwood Press, 2002. ISBN 0-313-32344-5
Fabre, Claire. "Aux frontières de l’intime : l’intériorité exhibée dans Room Temperature (1984) de Nicholson Baker." Revue française d’études américaines. 2006. 113-121.
Richardson, Eve, "Space, Projection and the Banal in the Works of Jean-Philippe Toussaint and Nicholson Baker", in Emma Gilby et Katja Haustein (ed.), Space. New Dimensions in French Studies, Oxford, Bern, Berlin, Brussels, Francfurt, New York and Vienna, Peter Lang, 2005. ("Modern French Identities", 30)
Saltzman, Arthur M. Understanding Nicholson Baker. University of South Carolina Press, 1999. ISBN 1-57003-303-X
Star, Alexander. "The Paper Pusher." The New Republic. May 28, 2001. 38-41.