I can't list why I like each series without going into tremendous amounts of detail. So to make up for that, I'll list my Top 25:
25. Rurouni Kenshin (1994~1999, Watsuki Nobuhiro)
24. Mobile Police Patlabor (1988~1993, Oshii Mamoru)
23. YAIBA (1988~1993, Aoyama Gosho)
22. Bobobo-Bo Bo-Bobo (2001~2007, Sawai Yoshio)
21. Shonan Junai Gumi/GTO (1991~present, Fujisawa Tooru)
20. Kochira Katsushika-ku Kameari Kouen-mae Hashutsujo (1976~present, Akimoto Osamu)
19. Sakigake!! Otokojuku (1985~1991, Miyashita Akira)
18. Lupin III (1967~present (sporadic), Monkey Punch)
17. Keroro Gunsou (1999~present, Yoshizaki Mine)
16. GeGeGe no Kitarou (1950s~present (sporadic), Mizuki Shigeru)
15. DRAGON BALL (1984~1995, Toriyama Akira)
14. History's Strongest Disciple Kenichi (2002~present, Matsuena Shun)
13. Eyeshield 21 (2002~2009, Itagaki Riichirou & Murata Yuusuke)
12. Hokuto no Ken (1983~1988, Buronson & Hara Tetsuo)
11. DEATH NOTE (2003~2006, Ohba Tsugumi & Obata Takeshi)
10. Detective Conan (1994~present, Aoyama Gosho)
9. Space Battleship Yamato (1972~1983, 2009!!!, Matsumoto Leiji)
8. Ranma 1/2 (1987~1996, Takahashi Rumiko)
7. Cyborg 009 (1964~1985 (sporadic), Ishinomori Shoutarou)
6. SLAM DUNK (1990~1996, Inoue Takehiko)
5. Urusei Yatsura (1978~1987, Takahashi Rumiko)
4. Kinnikuman (1979~1987, Yudetamago)
3. One Piece (1997~present, Oda Eiichirou)
2. Maison Ikkoku (1980~1987, Takahashi Rumiko)
1. Hajime no Ippo (1989~present, Morikawa Jouji)