Nabil,
Unfortunately, many PDFs do not "re-flow" properly on the nook. I have found that using Mobipocket Creator (install as publisher for PDF support) to convert from PDF to PRC and then Calibre to convert PRC to ePUB works much better for me. Once you have it converted to ePUB, you can use Sigil to clean up any remaining problems you may find with the document.
http://www.mobipocket.com/en/Downloa...ilsCreator.asp
http://calibre-ebook.com/
http://code.google.com/p/sigil/