There are so many good characters, it is hard to choose!
I think Ruki from Tamers and Ken from 02 are my favorites. Ruki is tough, but kind. I like how she reconnects with her mother and grandmother during the story and also forges such a deep bond with Renamon, all while keeping her steely resolve intact. Ken on the other hand starts off as a villain, but turns out to be such a gentle person who struggles with his inner darkness. I think his relationship with Wormmon is very moving and his friendship with Daisuke was another highlight.
Both these characters start out great and just get more interesting with time!
Oh my favorites are: all main 02 characters, Wallace, Menoa, Ruki, Hirokazu, Kouichi & Kouiji, Masaru & Ikuto, Taiki, All main Appmon characters, and Kiyoshirou.