These were my favorite manga the last time that I updated the list.

Favorite Manga Rating Comment
A.I. Love You (manga) Excellent
Ai Yori Aoshi (manga) Excellent #8
Alice on Deadlines (manga) Very good
Aqua (manga) Very good
Aria (manga) Very good
Azumanga Daioh (manga) Excellent
Buso Renkin (manga)
Cardcaptor Sakura (manga) Masterpiece #1
Cardcaptor Sakura: Master of the Clow (manga) Masterpiece #1
Case Closed (manga) Excellent #6
Chibi Vampire (manga by Y. Kagesaki) Excellent
Chikyu Misaki (manga) Excellent
Chobits (manga) Excellent
Dance in the Vampire Bund (manga) Excellent
Dream Saga (manga) Very good
Full Metal Panic! (manga) Very good
Fushigi Yûgi (manga) Very good
Gimmick! (manga) Very good
Girlfriends (manga) Excellent #10
Hanako and the Terror of Allegory (manga) Excellent
Happy Hustle High (manga) Very good
He is my Master (manga) Excellent
Hibiki's Magic (manga) Excellent
Hinadori Girl (manga) Excellent
Inukami! (manga) Very good
Inuyasha (manga) Masterpiece #3
K-ON! (manga) Masterpiece #2
K-ON! College (manga) Excellent
K-ON! High School (manga) Excellent
Kagetora (manga) Excellent
Kashimashi ~Girl Meets Girl~ (manga) Excellent
Kindaichi Case Files (manga) Excellent
Love Roma (manga) Excellent #7
Lucky Star (manga by K Yoshimizu) Good
Mahoromatic (manga) Excellent
Maid Sama! (manga) Excellent
Maniac Road (manga) Very good
(The) Melancholy of Haruhi Suzumiya (manga) Excellent #4
Pretty Face (manga) Excellent
Pretty Maniacs (manga) Very good
Princess Resurrection (manga) Very good
Ranma ½ (manga) Excellent #9
Rosario + Vampire (manga) Very good
Rosario + Vampire Season II (manga) Very good
Rumic Theater (manga) Excellent
School Rumble (manga) Excellent #5
Sgt. Frog (manga) Excellent
Shakugan no Shana (manga) Excellent
Shakugan no Shana (light novel) Excellent
Stray Little Devil (manga) Excellent
Sunshine Sketch (manga) Good
Tokyo Mew Mew (manga) Very good
Ultra Maniac (manga) Very good
Wedding Peach (manga) Very good