After giving it about an hour's thought, these are my top five titles for each season of 2000 to 2009. Top tens for seasons that made decisions hard for me.
Winter 2000
Boogiepop Phantom
Kazemakase Tsukikage Ran
Okamajo Doremi #
Miami Guns
Megami Kouhosei
Easy choices for me. This wasn't a great season for anime by any means.
Spring 2000
Furi Kuri
Banner of the Stars
NieA_7
Gatekeepers
Ayashi no Ceres
Summer 2000
Strange Dawn
Jin-Roh
Brigadoon - Marin to Meran
Card Captor Sakura Movie 2
Hand Maid May
Another bitzer season, this one.
Fall 2000
VanDread
Sci Fi Harry
Argento Soma
Blood - The Last Vampire
Yami no Matsuei
Winter 2001
Maetel Legend
Shin Getter vs Neo Getter
Time Stranger Kyoko
Earth Girl Arjuna
Motto Ojamajo Doremi
Pretty bog-standard season, this one.
Spring 2001
Jungle wa Itsumo Hale nochi Guu
Read Or Die
Figure 17 - Tsubasa and Hikaru
Super GALS Kotobuki Ran
Animation Runner Kuromi-chan
Noir
You're Under Arrest 2
Mahou Senshi Louie
Angelic Layer
Puni Puni Poemi
But it got better.
Summer 2001
Fruits Basket
Scryed
Banner of the Stars 2
Spirited Away
Alien 9
Fall 2001
Cowboy Bebop Movie
Chiyoko Millennial Actress
Hellsing
Kaze no Yojimbo
Hikaru no Go
Winter 2002
Fullmetal Panic!
Rah-Xephon
Onegai Teacher
Hoshi no Koe
Secret of Cerulean Sand
Spring 2002
Azumanga Daioh
Abenobashi Mahou Shoutengai
12 Kingdoms
WXIII Patlabor the Movie 3
Chobits
Summer 2002
Princess Tutu
The Cat Returns
SaiKano
Witch Hunter Robin
Yukikaze
Fall 2002
Haibane Renmei
Ghost in the Shell: Stand Alone Complex
Gundam Seed
Kiddy Grade
Overman King Gainer
Things were really easy to choose at about this point. It started getting harder from here on.
Winter 2003
Yokohama Kaidashi Kikou: Quiet Country Cafe
Mahou Tsukai no Taisetsu na Koto - Someday's Dreamers
Macross Zero
Gunparade March
Wolf's Rain
Spring 2003
Kino no Tabi: The Beautiful World
Scrapped Princess
Texhnolyze
Stellvia of the Universe
Kaleido Star
Last Exile
GadGuard
Hitsuji no Uta
Matantei Loki Ragnarok
Mermaid Melody Pichi Pichi Pitch
Summer 2003
Fullmetal Panic? Fumoffu
Tokyo Godfathers
NaruTaru
Nasu: Summer in Andalusia
Da Capo
Fall 2003
Planetes
R.O.D. the TV
Fullmetal Alchemist
Gunslinger Girl
Uninhabited Planet Survive
Winter 2004
Paranoia Agent
Maria-sama ga Miteru
Gokusen
Jubei-chan 2 - The Revenge of Siberia Yagyuu
Futari wa Precure
Spring 2004
Samurai Champloo
Monster
Mahou Shoujotai Alice
Innocence
Kenran Butou Sai - The Mars Daybreak
Summer 2004
Kurau Phantom Memory
Maria-sama ga Miteru Haru
Soukyuu no Fafner
Otogizoushi
Elfen Lied
It says how bad this past season was that Elfen Lied got into my top five.
Fall 2004
Gankutsuou
Fantastic Children
Beck
Genshiken
Beyond The Clouds
Windy Tales
Howl's Moving Castle
Mai-Hime
Rozen Maiden
School Rumble
Winter 2005
Starship Operators
Kino no Tabi - Life Goes On
Mahoraba
Shin Angyou Onshi
Ah My Goddess
Spring 2005
Zettai Shonen
Eureka Seven
Honey and Clover
Victorian Romance Emma
Basilisk
Summer 2005
Kamichu
Pani Poni Dash
Fullmetal Panic - The Second Raid
Ichigo Mashimaro
Okusama wa Mahou Shoujo
Fall 2005
Mushishi
Aria the Animation
Noein
Jigoku Shoujo
Magical Girl Lyrical Nanoha A's
Akagi
Mai-Otome
Paradise Kiss
Shakugan no Shana
Blood+
This was the "holyfarkingshite where did all these shows suddenly come from" season.
Winter 2006
Hellsing Ultimate
Pale Cocoon
Ergo Proxy
Rec
Kashimashi
And then it went quiet, again. After Kashimashi, the quality really dropped off.
Spring 2006
Higurashi no Naku Koro ni
The Melancholy of Haruhi Suzumiya
Aria the Natural
Black Lagoon
Simoun
xxx-HOLiC
Ouran High School Host Club
Saiunkoku Monogatari
School Rumble Ni Gakki
Strawberry Panic
The heart of 2006, for sure. Why I remember the year so fondly.
Summer 2006
The Girl Who Leapt Through Time
Welcome to the NHK
Honey and Clover II
Le Chevalier D'Eon
Kemonozume
Fall 2006
Code Geass
Black Lagoon: The Second Barrage
Death Note
Ghost Hunt
Soukou no Strain
Asatte no Houko
Paprika
Freedom
Maria-sama ga Miteru 3rd Season
Kanon
I keep saying: it isn't that Death Note is bad, it's just that its fans are zurückgeblieben.... Like narutard zurückgeblieben. You can't help but associate it with the worst aspects of fandom.
Winter 2007
Nodame Cantabile
Hidamari Sketch
5cm per Second
Rozen Maiden Ouverture
Manabi Straight
Spring 2007
Seirei no Moribito
Tengen Toppa Gurren Lagann
Lucky Star
Dennou Coil
Claymore
Summer 2007
Higurashi no Naku Koro ni Kai
Sayonara Zetsubou Sensei
Baccano
Potemayo
School Days
Fall 2007
Sword of the Stranger
Aria the OVA: Arietta
Moyashimon
Ghost Hound
Sketchbook: Full Color's
Minami-ke
Bamboo Blade
Shion no Ou
Genshiken 2
Nasu: Migratory Bird's Suitcase
This wasn't actually that great a season, but the shows were so blutig even at that second-string level that it made it hard to choose.... I had to reluctantly leave out Mokke, which really deserves to be amonst the bottom end of this list....
Winter 2008
Aria the Origination
Zoku Sayonara Zetsubou Sensei
True Tears
Spice and Wolf
Shigofumi
blutig Ariafag that I am.
Spring 2008
Kurenai
Code Geass R2
Tower of Druaga: The Aegis of Uruk
Allison to Lillia
Kaiba
Only just failed to make it: Toshokan Sensou
Summer 2008
Natsume Yuujinchou
Hidamari Sketch x365
Xam'd Lost Memories
Eve no Jikan
Mahou Tsukai ni Taisetsu na Koto: Natsu no Sora
Fall 2008
Mouryou no Hako
Ga-Rei Zero
Nodame Cantabile: Paris-hen
Hyakko
One Outs
Winter 2009
Zoku Natsume Yuujinchou
Maria-sama ga Miteru 4th Season
Kemono no Souja Erin
Birdy the Mighty Decode 2
Denpa Teki na Kanojo
Spring 2009
Eden of the East
Isekai no Seikishi Monogatari
K-ON!
Hayate no Gotoku 2
Cross Game
Summer 2009
Tokyo Magnitude 8.0
Summer Wars
Umineko no Naku Koro ni
Spice and Wolf 2
Cencoroll
Some tough choices, here.
Fall 2009
Aoi Bungaku
Kimi ni Todoke
Tatakau Shisho: The Book of Bantorra
Natsu no Arashi: Akinai-chuu
11eyes
And this last one almost made me cry. Looking back on all the other seasons, it was really only comparable to Winter 2000 in quality.... Where the 00's started.