While probably not as "serious" or "significant" on the whole as the anime titles that swept this category, I think a few of these could have been considered for inclusion or even been given an "honorable mention" that other shows were given in other categories.
Totally Spies! (2001) - One of the first western shows (from France) to parody anime during the post-Pokemon anime boom earlier this decade. Though some wished for a bit more character development (like me!), the series was usually well animated, fast-paced, and a real hoot! The lack of seriousness or many (or any) distinguished bad guys I think turned a lot of fans off as the series progressed, but I for one would love to see the girls show up on American TV again, especially since Season Five has yet to air here. I'm keeping my fingers crossed that the feature film prequel released this summer at least gets a US DVD release.
Braceface (2001) - This underappreciated Canadian series documents the trials and tribulations of a 13-year old girl, Sharon Spitz (voiced by Alicia Silverstone), as she tries to cope with family, friends, school, and boys. While adequately animated, the writing and plots are what really sets this series apart. It's obviously meant as a means to educate young girls about growing up, but it's done with so much humor, heart, and realism it doesn't come off as preachy in the least even when dealing with subjects like underage drinking, body image, or a first period. The show aired on the old Family Channel until the network was purchased by Disney and aired on Toon Disney a few years ago, though some episodes were not aired and with edits. The second half of Season Two and all of Season Three have yet to air in the U.S.
Code Loyko (2004) - This is probably the most well known of the shows I'm bringing up, but a lot still don't know about it. The use of both 2D and 3D animation in the show was striking and definately set it apart. Though Season 1 was a bit repetitive, the character interactions established during that time, along with the excellent two-parter that concluded the season, made it a fan favorite. The graphics improved as the series progressed, though the storyline and focus of the series kind of shifted around as it approached its current end. Though flawed, I think the series deserves to be considered in light of its uniqueness.
Monster Allergy (2005) - While Italian comic artist/producer Iginio Straffi's other two animated series (Winx Club and Huntik) have both been aired in their entirety in the U.S., this show only received a partial airing during the 2006-2007 season on the now cancelled KidsWB! weekend cartoon block. Less "poppy" than Winx Club and more comedic than Huntik, the series concerned a 12 year-old boy (Ezekiel Zick) whose allergies of monsters aid him in his efforts to become a Monster Tamer as was his missing father. The bond among the main characters in both Winx Club and Huntik pale in comparison to the one that developes between Ezekiel and Elena Potato, his new friend, as they hunt the monsters and attempt to hone Ezekiel's skills. A second season of 26 episodes has been aired in other parts of the world and I for one would like to see the show get a full run here in the U.S.
Class of the Titans (2005) - A group of teenaged decendents of Greek gods and their efforts to thwart the evil plans of Chronos the God of Time to conquer and destroy the world are the focus of this Canadian action/adventure series. Although it recently begain airing in the U.S., since it airs on Qubo's digital sub-channel, only a limited audience has access to the show.
Oban Star Racers (2006) - Creator Savin Yeatman-Eiffel spent five years pitching this series around the world resisting attempts to alter his vision before this French/Japanese co-production premiered in 2006. Hats off to his fortitude as the series, with it's "noseless" character designs, engaging mix of 2D animation and CG, and exciting and touching storyline, was one of the best shows of the year. Unfortunately, a large number of U.S. viewers never got to see it as it was broadcast on Toon Disney (now Disney XD) a network with a rather low cable prescence. The series is now available on DVD so everyone can discover just what they missed.
Di-gata Defenders (2006) - This Canadian adventure/fantasy series' first 26 episodes aired on the Fox 4Kids (now CW 4Kids) weekend block during 2007 and 2008. Although there are apparantly another 26 episodes available, it appears CW 4Kids has no plans to acquire and broadcast them. In fact, the parties that administer the 4KidsTV website have yet to upload all the broadcasted episodes while other shows have their entire run available for online viewing.
Grossology (2006) - Based on a series of children's books, this show is one of a few recent series that include educational and informational material without comprimising the humor and entertaiment value of the show itself. Exceptional writing and strong characters make this one of the better animated shows aired in the U.S. on Discovery Kids. A second season of 26 episodes are airing in Canada but have yet to show up in America. One can only hope we won't have to wait long for them to do so.