Ruegger married voice actress Adrienne Alexander in 1983; they have three sons together, Nathan, Luke and Cody.

Nathan voiced the baby version of Plucky Duck on Tiny Toon Adventures, Skippy Squirrel on Animaniacs and Froggo on Histeria, where Luke provided the voice for the Flame and Bumpo Basset on Animaniacs and Big Fat Baby on Histeria.

[14] Ruegger's sons also are the primary inspiration behind the main characters in Animaniacs, Yakko, Wakko and Dot.

[15] As of 2017, Cody is serving as an attorney in New York City,[16] while Nathan and Luke have careers in film and television in Los Angeles.

Ruegger himself also made occasional cameos on his shows in caricature form, most notably as the recurring character of director Cooper DeVille in Tiny Toon Adventures.