His 1999 instrumental solo album, Nonkertompf, prompted these comments by David Fricke in Rolling Stone magazine: "I saw guitarist Mike Keneally play with Frank Zappa in the 1980s, nimbly negotiating the maestro's knotty charts, and I've watched Keneally cook hard with his twisted-fusion outfit, Beer For Dolphins. But none of it prepared me for the color and density of Nonkertompf, a whirl of thirty-five instrumental miniatures, played by Keneally in their entirety and advertising not only his spicy fluency on the guitar but a flair for hot melodic sabotage rooted, yet not imprisoned, in Zappology.
The music flies mad and fast, but what the hell? You have a whole century to digest it."
In 2001, Dutch broadcaster NPS commissioned a triumphant orchestral performance and live broadcast of Nonkertompf featuring Keneally's seven-piece rock band augmented by four Dutch classical musicians.
Keneally's other releases include 1992's hat., 1994's Boil That Dust Speck, 1996's Half Alive In Hollywood and 1997's Sluggo!.