Hard to say, though my viewing over time drastically decline.
Seinen: Stand Alone Complex, with Bebop and NHK as runner-up. Honorable mention to Samurai Champloo, Gunmm, Jojo (s4), Trigun, and Berserk. GiTs is pretty much the mother of modern dystopian genre, the only genre in fiction I actually enjoy.
Shounen: HunterxHunter (2011), Eureka 7 and Soul Eater (manga) as runner up. Honorable mentions to One Piece, DB, Gurren Lagann, Detective Conan, and FMA. Though Eureka 7's first half-2/3rds was my favorite shonen.
Shoujo/Josei: Sailor Moon and Wolf's Rain (I like anything when Yoko Kanno is composing). Honorable mention to Akatsuki no Yona.
I've forgotten most I've seen though.