Some underrated films that come to mind:
Fritz the Cat (watched it a few years ago, it was so funny to watch. And I watched the sequel as well, which is not as great.)
The Mouse and His Child (as philosophical as it was, I found the movie enjoyable)
Dot and the Kangaroo movie series (Some sad scenes here and there, but still a good watch)
Down and Dirty Duck (like Fritz the Cat, but with a duck instead. This is basically an acid trip, with Yellow Submarine-like animation to boot)
Felidae (haven't watched it, and don't plan to, either. It's basically like Plague Dogs, but with cats, and since I love cats, I just couldn't watch it)
Once Upon a Girl (Hanna-Barbera actually made this back in the 70s, and is basically another animated porno film, with adult fairy tales)
Tarzoon: Shame of the Jungle (another animated porno, I admit it made me chuckle a little)
Twice Upon a Time (I loved Lorenzo Music's voice acting in this film as Ralph, the all-purpose animal)
Heavy Metal (great movie with some porn and some classic rock!)
Vuk (A Hungarian film about a little fox seeking revenge on two dogs, I watched this movie a lot as a kid)
DuckTales the Movie (I liked watching this film so much as a child, I think I watched it at least once a year, if not more)
Doug's First Movie (technically his only movie, but I love the premise, considering I grew up with Doug and other Nick/Disney shows)
Pooh's Grand Adventure (it stands out as the darkest movie in the Pooh franchise, and "Wherever You Are" made me cry every time)
Eight Crazy Nights (I know what you're thinking - this movie is bad. It is, but it still has some good jokes in there)
The Black Cauldron (I haven't seen too much of it, but it was considered the black sheep of Disney animated films due to how dark it was)
That's all I could think of at the moment.