Thought you would never ask. I've got an incomplete Anime and Manga Top 25.
The list is incomplete.
Top Ranked Manga Franchises
1. Naruto by Masashi Kishimoto (99.5/100) (Code Reference: NAR)
2. Mahou Sensei Negima by Ken Akamatsu (97.5/100) (Code Reference: MSN)
3. Ah! My Goddess/Ah! Megami-Sama by Kosuke Fujishima (96/100) (Code Reference: AMG)
4. Fullmetal Alchemist by Hiromu Arakawa (95.5/100) (Code Reference: FMA)
5. Fairy Tail by Hiro Mashima (94/100) (Code Reference: FTL)
6. Hayate no Gotoku/ Hayate the Combat Butler by Kenjiro Hata (93/100) (Code Reference: HNG)
7. Bleach by Tite Kubo (91/100) (Code Reference: BCH)
8. Sekirei by Gokurakuin Sakurako (90.5/100) (Code Reference: SKI)
9. Love Hina by Ken Akamatsu (90/100) (Code Reference: LHA)
10. Rosario to Vampire* (88.5/100) (Code Reference: RTV)
11.
12.
13. Kimi no Iru Machi by Seo Kouji (86/100) (Code Reference: KIM)
14. Cage of Eden by Yamada Keiyou (84/100) (Code Reference: COE)
15. Suzuka by Seo Kouji (83.5/100) (Code Reference: SUK)
16. Highschool of the Dead by Daisuke Sato and Shoji Sato (80.5/100) (Code Reference: HOD)
17. Mysterious Girlfriend X by Usehiba Riichi (80/100) (Code Reference: MGX)
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20 Fire Emblem: Hasha no Tsurugi by Izawa Hiroshi & Yamada Koutarou (75/100) (Code Reference: FET)
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Currently in the hopper: One Piece, Inuyasha, Shaman King, I''S, Sayonara Zetsubou Sensei, Black Lagoon, Bakuman, Air Gear.
To name a few.
Top Ranked Anime Franchises
1. Martian Successor Nadesico (99.5/100) (Code Reference: MaSN)
2. Mahou Sensei Negima (97/100) (Code Reference: MSN)
3. Naruto/Naruto Shippuden (94.5/100) (Code Reference: NAR)
4. Ah my Goddess (94/100) (Code Reference AMG)
5. Hayate no Gotoku/Hayate the Combat Butler (93/100) (Code Reference: HNG)
6. Rosario to Vampire (92.5/100) (Code Reference: RTV)
7. Full Metal Panic (92/100) (Code Reference: FMP)
8. Lucky Star (91.5/100) (Code Reference: LST)
9. Fullmetal Alchemist/Fullmetal Alchemist Brotherhood (91/100) (Code Reference: FMA)
10. Bleach (90.5/100) (Code Reference: BCH)
11. Fairy Tail (90/100) (Code Reference: FTL)
12. Nagasarete Airantou (89.5/100) (Code Reference: NAU)
13. Bamboo Blade (89/100) (Code Reference: BBE)
14. Zoids (88/100) (Code Reference: ZOD)
15. Gundam (85/100) (Code Reference: GDM) (Gundam is special, for each different series, for instance, wing, would be Code Reference: GDM:W)
16. Dragonball Z (84/100) (Code Reference: DBZ)
17. Love Hina (82/100) (Code Reference: LOH)
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The Negima ones are heavily based on the OADs.
Currently in the Hopper: One Piece, Inuyasha, Shaman King, Slayers, Axis Powers Hetalia, Cowboy Bebop, Claymore, Death Note, Da Capo, Code Geass, Ef a Tale of Memories, Elfen Lied, Eureka Seven, FLCL, Green Green, Hellsing, Heroic Age, Nadia the Secret of Blue Water, Matantei Loki Ragnarok, Outlaw Star, Pandora Hearts, Ranma 1/2, Queen's Blade, Planet ES, Rosen Maiden, Sacred Blacksmith, Sayonara Zetsubou Sensei, Seolpm no Qwaser, Soul Eater, To Love-RU, Toradora, Trigun, and Tsubasa Reservoir Chronicles.
To name a few.