Mobipocket creator ( http://www.mobipocket.com/en/DownloadSoft/default.asp?Language=EN ) is the best software i've seen so far that can convert a pdf file to mobi in very good quality. My opinion, it is much better than calibre ( http://calibre-ebook.com/ ), another ebook format conversion software.
Kindle fans know that kindle supports pdf poorly. I personally feel kindle supports .mobi as good as its own .azw. At least i haven't found any difference between them. They both bring me same comfortable reading experience.