There are several anti Islamic sites out there that criticize the way the Prophet dealt with the Jewish tribes of Madinah. I am only providing a list of references that Muslims could appeal to and might find helpful if they are ever in a situation in debating the issues or answering the inquiries of a curious non Muslim.
The Banu Nadir
http://www.bismikaallahuma.org/index.php/articles/the-expulsion-of-banu-al-nadir (good article)
http://www.faithfreedom.com/ali_sina_exposed/truth_about_jews.htm (talks about all the Jewish tribes)
http://www.ispi-usa.org/muhammad/muhammad11.html (talks about all the Jewish tribes)
http://www.usc.edu/dept/MSA/history/biographies/sahaabah/bio.MUHAMMAD_IBN_MASLAMAH.html (talks a bit about the tribe near the end of the article)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_31.html (talks about the Jewish tribes)
http://www.thewaytotruth.org/prophetmuhammad/trench.html (talks about Banu Qurayza and Banu Nadir)
http://www.theambition.com/details.asp?article=41 (talks about Banu Nadir's role in attacking the Muslims)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_21.html (General information on all the Jewish tribes)
http://www.islamonline.net/english/science/2004/04/article05.shtml (talks about why the Prophet ordered the cutting of the Palm Trees when invading Banu Nadir)
The Banu Qaynuqa
http://www.bismikaallahuma.org/index.php/articles/the-expulsion-of-banu-qaynuqa (excellent article)
http://www.mostmerciful.com/prejudiced-partial.htm (there is a small part regarding the Qaynuqa, but the article is interesting)
http://www.faithfreedom.com/ali_sina_exposed/truth_about_jews.htm (talks about all the Jewish tribes)
http://www.ispi-usa.org/muhammad/muhammad11.html (talks about all the Jewish tribes)
http://www.islamicthought.org/sril-2002/sril-2002-mapp.html (talks very briefly about the tribe)
http://www.islamic-council.org/lib/first-muslim-states/allch3/CHAPTER3.html (talks very briefly about the tribe)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_19.html (short but informative)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_31.html (talks about the Jewish tribes)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_21.html (General information on all the Jewish tribes)
The Banu Qurayza
http://www.bismikaallahuma.org/index.php/articles/the-expulsion-of-banu-al-qurayzah (excellent article)
http://www.bismikaallahuma.org/index.php?s=banu (interesting)
http://www.mostmerciful.com/prejudiced-partial.htm (there is a small part regarding the Qurayza, but the article is interesting)
http://www.faithfreedom.com/ali_sina_exposed/truth_about_jews.htm (talks about all the Jewish tribes)
http://www.islamvision.org/BanuQuraizah.asp (informative)
http://www.ispi-usa.org/muhammad/muhammad11.html (talks about all the Jewish tribes)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_31.html (talks about the Jewish tribes)
http://www.thewaytotruth.org/prophetmuhammad/trench.html (talks about Banu Qurayza and Banu Nadir)
http://www.hizb-ut-tahrir.org/english/books/state/chapter_21.html (General information on all the Jewish tribes)
source :www.answering-christianty.com