Here are a few Japanese polls of best manga:
http://fischer.hosting.paran.com/comics/50best/50bestinfoE.htm
http://comipress.com/news/2007/06/08/2082
http://www.manganews.net/forums/showthread.php?t=2625
http://comipress.com/news/2006/04/03/6
http://www.animenewsnetwork.com/news/2005-11-07/oricon-ranks-top-10-shoujo-manga

This looks like it might be another one, but Google translation is incomprehensible:
http://kajipon.com/manga-d.htm
Are there any Japanese speakers here who'd like to translate that?

Does anyone have more lists like these? Thanks in advance!