Jones' best-known work is The Fantasticks, which ran off-Broadway from 1960 until 2002, and the hit song from the same, "Try to Remember". Other songs from The Fantasticks include "Soon It's Gonna Rain", "Much More" and "I Can See It". He also wrote the screenplay for the 1995 feature film adaptation.
Jones acted in a New York City revival of The Fantasticks, which he also directed. He played the part of the Old Actor, which he played when the musical opened in 1960, from April 26, 2010, to June 6, 2010. He was credited as an actor in the show as Thomas Bruce.
Jones is also the author of Making Musicals: An Informal Introduction to the World of Musical Theater, about which Elyse Sommer wrote on January 15, 1998 in CurtainUp:
- Extremely well organized and packed with interesting information, the first half of the book deals in broad and general terms with the growth and development of the American musical. The second half focuses on the practical "how-to" of putting together a musical, using Jones's own career and shows he's worked on as a springboard ... Since only half the book falls within the category of how-to I'm glad to report that this advice is stick-to-the-ribs solid. No hyperbole. No gratuitous name dropping.
- Shoestring '57 (contributor) (1957)
- Demi-Dozen (contributor) (1958)
- The Fantasticks (1960) 
- 110 in the Shade (book by N. Richard Nash, based on his play The Rainmaker) (1963)
- I Do! I Do! (based on The Fourposter by Jan de Hartog) (1966)
- Celebration (1969)
- Colette (1970)
- Philemon (1973)
- Grover's Corners (based on Our Town) (1987)
- Mirette (book by Elizabeth Diggs, based on the children's book Mirette on the High Wire by Emily Arnold McCully) (1996)
- Roadside (book by Jones, based on the 1929 play of the same name by Lynn Riggs, with music by Harvey Schmidt) (2001 off-Broadway (York Theatre))
- Harold and Maude (2004; music by Joseph Thalken, based on the film)
- The Game of Love (music by Offenbach with arrangements and additional music by Nancy Ford, based on the Anatol plays by Arthur Schnitzler).
- Hetrick, Adam. 2010-06-04. Tom Jones to Depart the Fantasticks Off Broadway. Archived August 8, 2010, at the Wayback Machine
- Brantley, Ben. 2006-08-24. A Return to Off Broadway, With Performance No. 17,163. The New York Times.
- Making Musicals: An Informal Introduction to the World of Musical Theater, (Paperback) 1998, Limelight Editions.
- Making Musicals Review by Elyse Sommer, January 15, 1998, CurtainUp.