I hear that the Care Bears comic series explained the presense of Gramms, Hugs and Tugs.
Plus, Avengers United They Stand, go into the background of Ultron. As well as Hawkeye and Wonder Man. Even explains the reason for the armor.
While these comics are 100% canon they are accepted as such:
Batman Gotham Adventures #4- Explains the change of Catwoman's appearance in The New Batman Adventures.
Batman Gotham Adventures #6- Deadman's first animated style appearance. The story is referenced in the Justice League Unlimited episode "Dead Reckoning".
Batman Beyond #21- Whether or not the story fits, it does give us the name of that era's Green Lantern which is Kairo (the name of Hal Jordan's sidekick in the three Green Lantern cartoons by Filmation).
Just a little tidbit concerning Gargoyles. While the Marvel Comics series is not canon, it does feature the appearances of Petros Xanatos and Beth Maza's full appearance prior to their episode debut.
Tale Spin #7 (the final issue, btw) goes a little more into Kit's background. The comic would have further explored the other characters as well. Plus the planned, but unmade Tale Spin Annual would have detailed the making of The Iron Vulture.