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Disclaimer: The following are links to other sites. We may not necessarily agree with all their content. 

Answering-islam.org A Christian but a very  comprehensive sites on the web. There is a wealth of material on Islam and Quran. 
Answering-islam.org.uk This is the mirror site of Answering Islam in UK.
Secularizing Islam by Ibn Warraq  One of the best sites for liberal views on Islam. (highly recommended)
Islamic Sharia Law 
Muhammad and his personal enemies
Muhammad's letter to the Julanda Brothers of Oman
Muhammad and Idolatry
Treaties
Muslim tradition on Heraclius' response to Muhammad's invitation
About the death of Muhammad
The Satanic Verses
Muhammad's Suicide Attempts
God's Last Messenger (?)
Homa.org  The Dr. Homa Darabi Foundation.
About.com Critiques of Islamic religious theology - including the hajj, jihad, apostates, hell and other concepts.
Sword of Truth  Excellent Hindu website; good material on the writings of the great Anwar Shaikh, and Islam in India
Anwar Shaikh  A Hindu site devoted to Anwar Shaikh’s highly original and very critical articles on Islam, Islamic Imperialism, Islamic violence and sex.
Documenting the Persecution of Christians in the Islamic World It links the persecution to Quran and teachings of Islam.
danielpipes.org  An authoritative commentator on Middle East
Resource Links 
Save Kashmir Movement.org
Freethoughtmecca A satirical site on Islam.
hraic.org Committed to combat Human Right abused in Islamic Countries 
Satyameva Jayate Good articles about the Prophet, women, terrorism, hell and other Islamic concepts.
The Islamic Monitor  This site warns the west of Islamic expansionism and the threat that it represents for freedom of speech and Western values.
New Horizons  Iranian outreach program in Southern California. New Horizons aims to promote the ideals of secularism, democracy, and rational inquiry to people of Iranian
Religious Tolerance  This site aims to promote religious diversity covering a dozen of religions, explaining controversial topics and both positive and negative aspects of religions.
Islamic Studies, Islam, Arabic, and Religion A site, posted by a University of Georgia professor, which is "intended to be of use for students and teachers at all levels, as well for members of the general public who wish to get a non-polemical view of Islam (including Sunni Islam, Shi'ism, and Sufism) and to a lesser extent of Judaism and Christianity."
The Internet Islamic History Sourcebook A wide-ranging collection of links pertaining to the Koran and Islamic history.
Universal Declaration of Human Rights 
The Treatment of Jews in Arab/Islamic Countries By Mitchell Bard
Atheist Evangelist 666  A place to learn about freethinking and humanism. 
Reform Islam  Various informative articles about Islam
Islamaniacs  Covers subjects like Islamic history, terrorism, totalitarianism, taboos, women and science
Denis Giron  Giron is a freethinker and writes very well. His articles include science and Islam, Muhmmad's idea of hell, etc.
Taslima Nasrin's page Another apostate carrying a death sentence for standing for women's rights in her homeland Bangladesh. 
Koran: Testimony of Antichrist a Christian site
New Secularism in the Arab World by Ghassan F. Abdullah It is wrongly assumed that there are few secular minded people within the Islamic world. Abdullah's article mentions many people and writings who dared to challenge Islam.
What is the Koran?" by Toby Lester Researchers with a variety of academic and theological interests are proposing controversial theories about the Koran and Islamic history, and are striving to reinterpret Islam for the modern world. This is, as one scholar puts it, a "sensitive business."
http://www.indian-skeptic.de/html/is_v02/2-3-10.htm Learned Questions is a quick review of Salman Rushdie's Satanic Verses by an Indian Skeptic.
Jihad and Civilization - Part 1 (The Battle of Badr) Anwar Shaikh, an ex-Muslim, discusses the true meaning of Jihad (Jehad). Shaikh cites the battle of Badr between Muhammad's followers, and an army of Arab warriors there to protect a commercial caravan. For related material, see Shaik's book 
Jehad By Anwar Shaikh
Negationism and the Muslim Conquests"  by Francois Gautier Gautier discusses negationism, which he defines as "the denial of historical crimes against humanity", in Muslim-Hindu conflict. The article classifies the Muslim invasion of India as a Holocaust inflicted on the Hindu "infidels".
Muslim Atrocities (Disturbing pictures of fanatical Muslim's brutalities) 
World Changer's Resource Page 
The Challenge of Islam 
Lamentations of a Muslims wife 
The Islamic revolution's impact on the legal and social status of Iranian women 
A Declaration of Women's Rights in Islamic Societies (1997) 
 The Islamic Threat to Global Security
Exposing Islam Page By  Cornholio
Metaphysical Naturalism 
Religious Fanatics 
Jeremiah McAuliffe & Abdul Saleeb- ( Muslim convert v.s. Caholic Convert)
Collection of Hadithes Muslim/Christian debate
http://www.thekoran.com/ Very good recourse on Islam
The Debate Site Muslim/Christian debate
Light of Life Investigate Islam from Christian point of view
Islam: The Way, The Truth and The Light? Islamic studies in Christian Perspective
Islam Unveiled Articles on the Prophethood of Muhammad, sources and errors of Quran, women and apostasy.
The Tougher Answers
Muhammadanism
Truthnet: Islam
The Quran.com
Islam Review  The Pen vs. the Sword
Islam Examined
Critical Analysis of Islam
Testimonies of Muslims who became Christians
Contradictions in the Qur'an
The Koran
What is Islam. What Do Muslims Believe?
Plain Truth About Islam  
The Official site for the persecution of Copts in Egypt 
The Fallacy of Islamic Tolerance In Religion
Amnesty International: Publications on Saudi Arabia (the Kingdom of)
Cultbusters.com By Robert Morey
Atlantic Monthly's article on the origins of the Koran  
Turan Dursun: The Trukish Freethinker (in English) 
Hülagü'nün Şeriat Karşıtı Web Sitesi HOŞGELDİNİZ  (In Trukish)
More Links

http://honestreporting.com/a/links.asp http://www.frontline.org.za/articles/articles/holy_war.htm www.standwithus.com http://www.ou.org/audio/video/jihad.ram http://www.yahoodi.com/peace/index.html http://www.pakistanchristianpost.com/index.php http://www.flex.com/~jai/satyamevajayate/hell.html www.pmw.org.il http://debate.org.uk/topics/history/home.htm http://answering-islam.org/Quran/Versions/009.030.html http://www.answering-christianity.com/expose_lies.htm http://members.aye.net/~abrupt/house/islam.html www.helpingisrael.com www.walk4israel.com www.mediawatch.com http://www.suntimes.com/output/steinberg/cst-nws-stein09.html http://www.wzo.org.il/en/resources/view.asp?id=222 Jersalem timeline http://www.frontline.org.za/articles/articles/holy_war.htm ISLAM sucks--2 worlds http://www.islamamerica.org/articles.cfm?article_id=28 http://www.secularislam.org/index.html http://israelvisit.co.il/BehindTheNews/index.html http://www.nytimes.com/2001/09/05/opinion/L05DURB.html http://archive.nandotimes.com/noframes/story/0,2107,500213544-500301401-5016 66124-0,00.html