Pretty much this will be like Naz's RPA's Top 100 Books, RPA's Top 100 Television Shows, RPA's Top 100 Musical Acts, RPA's Top 100 Video Games, and RPA's Top 100 Movies threads. 
Here is a list of my own personal top ten manga. 
- Fruits Basket - I am embarrassed to say I love this series? But oh well.
- Kare Kano - Another equally awesome romance story.
- One Piece - Scores a little higher then the other shonen manga because for me it is so much fun. It looks like it will never end, but for me that is part of the charm.
- Berserk - I enjoyed the story a lot when I was younger, back when I thought violence was cool. Now though it seems like the author is going to croak before the series is ever finished.
- Scott Pilgrim - What this isn't a manga? I don't care I am including it anyway! As far as I am concerned it can be considered both.
- Street Fighter - I'm a big fan of all the different Street Fighter comics that has came out of Japan. Including the Ryu Final.
- Rave Master - This manga is seriously underrated, probably because the Anime was so god awful. The manga is a million times better.
- Naruto / Naruto Shippuden - This series does seem to be a bit better then it has been. I eagerly look forward to the new chapter when it is released.
- Bleach - I don't love it as much as One Piece, but I still read it on a regular basis. In my opinion the art work is better then One Piece and Naruto.
- High School of The Dead - Maybe it is just the zombie fan of me, but I just felt the need to include this in.
Top 100
(note that games with only one post are in the order which they were submitted)
1 Scott Pilgrim(2)
2 Naruto / Naruto Shippuden (2)
3 Fullmetal Alchemist(2)
4 One Piece(2)
5 Berserk (2)
6 Rave Master (2)
7 One Piece
8 Fruits Baskets
9 Street Fighter
10 Kare Kano
11 Bleach
12 High School of The Dead
13 Berserk
14 Bastard!!
15 7 seeds
16 Inuyasha.
17 Claymore
18 D. Gray Man
19 Samurai Deeper Kyo
20 Red River
21 Angel Sanctuary
22 Breath of fire 4
23 Negima! Magister Negi Magi
24 Gantz
25 Histories Strongest Disciple Kenichi
26 Dengeki Daisy.
27 Crazy Girl Shin Bia
28 Sad Love Story
29 Kuroshitsuji
30 Black Bird
31 Ouran High School Host Club
32 Another
33 Are You Alice?
34 Tsubasa Reservoir Chronicles
35 Fate/Stay Night
36 Pokemon Special/Adventure
37 Soul Eater
38 Ultimo
39 Trigun
40 xxxHOLiC
41 Zatch Bell
Updated to fix Berserk and Rave Master mistake. Rave master was accidentally added twice at position 6 and 35.
RPA's Top 100 Manga
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