A topic series started by musumane, but later continued by superangelo128.
Apparently the original intent was to do shounen series but superangelo128 expanded it to visual novel routes, visual novel arcs, random other anime/manga arcs, and anime seasons.
Long-running Shounen Series[]
Fairy Tail: Fighting Festival, Runner up: Tenrou Island
Naruto Pre- Timeskip: Chuunin Exams, Runner Up: Land of Waves
One Piece: Water 7/Enies Lobby, Runner Up: Alabasta
Dragon Ball Z: Cell Saga, Runner Up: Frieza Saga
Bleach: Soul Society, Runner Up: Vandenrich/1000-Year War
Negima: Magic World, Runner Up: School Festival
Claymore Pre-Time Skip: Battle of the North, Runner Up: Teresa of the Faint Smile
Rave Master/Groove Adventure Rave: King/Tower of Din, Runner-Up: Mermaid
Dragon Ball: Piccolo Daimou/King Piccolo, Runner-Up: Red Ribbon Army
Rurouni Kenshin: Kyoto arc, Runner-Up: Trust and Betrayal/Tsuiokuhen
Jojo's Bizarre Adventure: Part 2 Battle Tendency, Runner-Up: Part 4 Diamond is Unbreakable
Naruto Post-Time Skip: Invasion of Pain, Runner-Up: Hidan and Kakuzu
Hunter x Hunter: Chimera Ant, Runner-Up: Yorknew City
Yu Yu Hakusho: Dark Tournament, Runner-Up: Chapter Black
Other Series[]
Humanity Has Declined: The Fairys Survival Skills, Runner Up: The Fairies Time Management
Digimon Adventure/Season 1: Myotismon Saga, Runner Up: Dark Masters Saga
Amagami SS: Ai Nanasaki arc, Runner Up: Haruka Morishima arc
Kanon 2006: Makoto Sawatari arc, Runner Up: Mai Kawasumi arc
Yu-Gi-Oh Duel Monsters: Battle City, Runner Up: Waking the Dragons/Orichalcos
Toriko: Century Soup, Runner Up: Mellow Cola/Cooking Festival
Tengen Toppa Gurren Lagann: Lagann-hen, Runner-Up: Post-Time Skip in original series
Digimon Adventure 02/Season 2: Digimon Emperor/Kaiser, Runner-Up: Destiny Stones
The World God Only Knows (what anime's covered): Shiori Shiomiya arc, Runner-Up: Tenri Ayukawa arc
Mirai Nikki: 11th/Akise Aru arc, Runner-Up: Yuno arc
Sailor Moon: Death Busters arc, Runner-Up: Dark Kingdom arc
Yu-Gi-Oh GX: Darkness arc, Runner-Up: Dimension World arc
Black Lagoon: Hansel and Gretel, Runner-Up: Japan
To Aru Majutsu no Index: Sisters, Runner-Up: Academy City Invasion
Haruhi Suzumiya (anime only no side stories): Disappearance, Runner-Up: Endless Eight
-monogatari series: Tsubasa Cat, Runner-Up: Nekomonogatari Black/Kuro
Busou Renkin: Papillion arc, Runner-Up: L.X.E and Kazuki Re-Extermination TIED
Code Geass: Ragnarok/Emperor Lelouch, Runner-Up: Euphinator
World God Only Knows (manga-only pre-godesses): Body Switch/Yui Goldo, Runner-Up: Ramen Girl/Sumire Uemoto
Futari wa Precure: Movie 2/Ice Twins, Runner-Up: Stuff before Porun appears
Kara no Kyoukai: 5: Mujun Rasen/Paradox Spiral, Runner-Up: 3: Tsuukaku Zanryuu/Remaining Sense of Pain
Pretty Cure Splash Star: TIE between Kintoleski and Akudaikan
Pokemon anime: Diamond&Pearl/Sinnoh, Runner-Up: Season 1/Kanto
Yu-Gi-Oh 5Ds: Dark Signers, Runner-Up: TIE between Fortune Cup and WRGP
Kaiji: E-card, Runner-Up: Bog
Heartcatch Precure: Dune arc, Runner-Up: Blossom/Marine and Sunshine TIED
World God Only Knows Awakening the Goddesses: Mercury, Runner-Up: Mars
Evangelion: End of Evangelion, Runner-Up: Episodes 8-18
Best Seasons[]
Sayonara Zetsubou Sensei: Season 1, Runner-Up: Zan
Hidamari Sketch: x Hoshimittsu, Runner-Up: x 365
Slayers: NEXT, Runner-Up: Season 1
Major: Season 1, Runner-Up: Season 5
Maria-sama ga Miteru: Season 1, Runner-Up: Season 2/Haru and 3rd TIED
Visual Novels[]
Higurashi no Naku Koro ni: Episode 6: Tsumihoroboshi/Atonement, Runner Up: Episode 5: Meakashi/Eye Opening
Muv-Luv Extra: Marimo route, Runner Up: Sumika route
Katawa Shoujo: Rin route, Runner Up: Hanako route
Ever17: Coco route, Runner-Up: Tsugumi route
Tsukihime: Kohaku route, Runner-Up: Hisui route
Clannad: After Story, Runner-Up: Tomoyo OVA/route
Sharin no Kuni: Chapter 5, Runner-Up: Houzuki Fandisc chapter
Umineko no Naku Koro ni: Episode 3: Banquet, Runner-Up: Episode 4: Alliance
G-senjou no Maou: Chapter 5/Haru, Runner-Up: Chapter 4 excluding Mizuha
ef: RenjixChihiro, Runner-Up: YuuxYuuko
Little Busters VN: Refrain, Runner-Up: Haruka route
Muv-Luv Alternative: PTSD arc, Runner-Up: Original Hive arc
Cross+Channel: Miki route, Runner-Up: Week 6
Hoshizora no Memoria: ***/??? Route, Runner-Up: Komomo route
Sengoku Rance: True History route, Runner-Up: Kenshin route
Crescendo: Ayame route, Runner-Up: Miyu and Yuka route TIED
Deus Machina Demonbane: Al Azif route, Runner-Up: Ruri Hadou route
Saya no Uta: Ending C, Runner-Up: Ending B
Symphonic Rain: Al Fine, Runner-Up: Phorni route
Rewrite: Moon, Runner-Up: Akane route
Yume Miru Kusuri: Aeka route, Runner-Up: Mizuki Route
Fate/Stay Night: Unlimited Blade Works, Runner-Up: Heaven's Feel