Here is the manga sales ranking for the first half of the fiscal year 2009 (November 17th, 2008 - May 17th, 2009).

*1, 1,801,877 One Piece vol.53
*2, 1,778,239 One Piece vol.52
*3, 1,418,089 NANA vol.21
*4, 1,170,718 Fullmetal Alchemist vol.21
*5, 1,131,145 Naruto vol.45
*6, 1,068,430 Fullmetal Alchemist vol.22
*7, *,927,610 Bleach vol.36
*8, *,907,714 Bleach vol.35
*9, *,864,708 Naruto vol.46
10, *,822,238 Bleach vol.38

11, *,685,186 Kimi ni Todoke vol.8
12, *,677,411 Saint Young Men vol.3
13, *,619,501 Kuroshitsuji vol.6
14, *,611,100 D.Gray-man vol.17
15, *,598,192 Katekyo Hitman Reborn! vol.23
16, *,593,589 Detective Conan vol.64
17, *,589,656 Pluto vol.7
18, *,572,946 Vagabond vol.29
19, *,557,839 Gintama vol.26
20, *,493,768 Katekyo Hitman Reborn! vol.24

21, *,551,920 Glass Mask vol.43
22, *,545,496 Gintama vol.27
23, *,493,768 Gintama vol.28
24, *,465,760 xxxHOLiC vol.14
25, *,441,939 3 Gatsu no Lion vol.2
26, *,402,965 Moyashimon vol.7
27, *,394,567 Bakuman vol.2
28, *,381,633 Bakuman vol.1
29, *,376,340 Hayate The Combat Butler! vol.18
30, *,374,257 Ouran High School Host Club vol.14

Source: Oricon comic ranking