As many have mentioned, Rocko's Modern Life was a biggie. Many Nicktoons had their moments, but there are others like the Animaniacs and other WB Television Animation shows, and the early Cartoon Cartoons(look at Johnny Bravo or Cow And Chicken for instance). Come to think of it, if it was a comedy cartoon in the 90's, chances are it had innuendos at one point in time.