In June, 2009, Jay Lynch was nominated for a Harvey Award in the category of "Best Cover Artist" for his Mineshaft #23 cover.

Lynch's best known comic book stories involve the human-cat duo, Nard n' Pat, the featured characters in Bijou Funnies. For 17 years, the comic strip Phoebe and the Pigeon People by Lynch and Gary Whitney, ran in The Chicago Reader, through the 1970s and 1980s, and Lynch has scans of more than 500 of those strips ready for any publisher who sees the potential of a Phoebe and the Pigeon People book.

Beginning in 1968, Lynch became a major contributor to Topps' Wacky Packages and Garbage Pail Kids, plus other Topps humor products. In 2002, he recalled his creative working methods and procedures with Len Brown and others at the Topps' Product Development Department:

During the 1990s, he began writing for Mad, and he also devised products for Mad merchandising.

Bijou Funnies was collected in the 1980s in the book, The Best of Bijou Funnies.

His children's book, Otto's Orange Day (Toon Books, 2008), a collaboration with Syracuse political cartoonist Frank Cammuso, is described by the publisher: "When Otto the cat meets a magical genie, he knows just what to wish for: he makes the whole world orange! At first, this new, bright world seems like a lot of fun, but when his mom serves orange spinach for lunch, Otto realizes that his favorite color isn’t the best color for everything. Fixing this mixed-up world won’t be easy though because Otto already used up his only wish."

Greg McElhatton (Read About Comics) reviewed:

Another collaboration, Mo and Jo Fighting Together Forever by Lynch with Dean Haspiel, was published by Toon Books in fall 2008. Toon describes this superhero satire: "Mona and Joey can't stop fighting! When the Mighty Mojo decides to give his powerful costume to them, these argumentative twins fight so much they rip it in half. Now each one is only half as strong! Can Mo and Jo find a way to combine their powers, fight the evil Saw-Jaw and save their town?"

Lynch was the cover story of The Comics Journal #114 (February 1987) which featured an extensive interview, "Jay Lynch and the Free Exploration of Ideas: An Interview," covering his life and career in detail. Lynch created a caricatured self-portrait for the cover illustration.

Undergrounds (edited)

• Bijou Funnies
• Turned On Cuties
• Roxy Funnies (1972)
• Pro Junior
• Purple Cat
• Nard n' Pat

Undergrounds (contributed)

• Bogeyman
• Fucked Up Funnies
• Gothic Blimp Works
• Radical America

Children's books

• Otto's Orange Day (2008)
• Mo and Jo (2009)

Comic strip

• Phoebe and the Pigeon People with Gary Whitney (17-year run in Chicago Reader)