It's unknown if he's dead or if he and his wife divorced. In Operation: C.A.K.E.D.-F.O.U.R., Numbuh 2 spoke of him in past tense for much of the episode, and Mr. Gilligan never appeared in person, speaking only in spirit. However, Mrs. Gilligan spoke of him in present tense in the final part of that episode, saying "Not you too, Hoagie!," so it can be assumed that he probably is alive.
Voiced (in characters' thoughts) by Jeff Bennett. He is in the comic Operation: T.R.I.K.E. but his face is never shown.