Based on the year that the anime ended and not the start of it: Ranked #1 to #3
2000: CardCaptor Sakura, Great Teacher Onizuka, Gakkou no Kaidan
2001: Fruits Basket (the Worst Year for Anime as I couldn't make a Top 3)
2002: Hajime no Ippo, Haibane Renmei, Azumanga Daioh
2003: Full Moon wo Sagashite, Princess Tutu, Kidou Senshi Gundam SEED
2004: Planetes, Fullmetal Alchemist, InuYasha
2005: Koukaku Kidoutai: Stand Alone Complex 2nd GIG, Monster, Full Metal Panic! The Second Raid
2006: Hachimitsu to Clover II, Mushushi, Eureka 7
2007: Tengen Toppa Gurren Lagann, Higurashi no Naku Koro ni Kai, Baccano!
2008: Aria the Origination, Natsume Yuujinchou, Code Geass: Hangyaku no Lelouch R2
2009: Clannd: After Story, Kemono no Souja Erin, Ookami to Koushinryou II
*Only superior entries of the same franchise added i.e. the best sequel/prequel listed unlike the other one I made.
** Bold denotes also in my Top 10 Faves.
*** List does not include Movies/OVAs/Specials.
While making this list, I also realized that the Golden Years of Anime had been between 2006 to 2011. I got headache trying to pick my Top 3 from these years.
Special Mentions (Not in any order): Aria The Animation (2005), Hachimitsu to Clover (2005), Rozen Maiden: Träumend (2005), Air TV (2005), Glass no Kamen 2005 (2006), Ouran Koukou Host Club (2006), Nana (2006), Aria the Natural (2006), Black Lagoon (2006), Higurashi no Naku Koro ni (2006), Suzumiya Haruhi no Yuuutsu (2006), NHK ni Youkoso! (2006), Zero no Tsukaima (2006), Death Note (2007), Code Geass: Hangyaku no Lelouch (2007), Kanon 2006 (2007), Nodame Cantabile (2007), Seirei no Moribito (2007), Ookiku Furikabutte (2007), Eikoku Koi Monogatari Emma: Molders-hen (2007), ef: A Tale of Memories. (2007), Lucky☆Star (2007), Romeo x Juliet (2007), Hayate no Gotoku! (2008), D.Gray-man (2008), Kidou Senshi Gundam 00 (2008), Clannad (2008), Ookami to Koushinryou (2008), Toshokan Sensou (2008), Nodame Cantabile: Paris-hen (2008), ef: A Tale of Melodies. (2008), Kuroshitsuji (2009), Toradora! (2009), Kidou Senshi Gundam 00 Second Season (2009), Skip Beat! (2009), Hajime no Ippo: New Challenger (2009), Zoku Natsume Yuujinchou (2009), Higashi no Eden (2009), K-On! (2009), Hayate no Gotoku!! (2009), Hatsukoi Limited. (2009), Suzumiya Haruhi no Yuuutsu S2 (2009).
nb. <<My list of 2010-2019 is here>>
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