Here's one character I can think of. In this case he was in a Manga adapted from the Anime. N'Xau who was in Mobile Suit Gundam: The Origin, a Manga adapted from the first show.
There were quite a few Fruits Basket characters not in the anime. Rin, Ren, Kureno, Machi, and Kakeru are the main ones that I can think of at the moment.