Liberal Islam.net

A collection of articles on progressive Islamic theology, by Zeeshan Hasan.
http://www.liberalislam.net/

What is Islam?

A discussion of philosophical aspects of science, Islam and the existence of God.
http://www.geocities.com/Athens/Troy/7568/index.html

Islamic Philosophy Online

Dedicated to the academic study of the philosophical output of the Muslim world. Includes bibliography, articles, dictionary, forum, and details of their publications.
http://www.muslimphilosophy.com/

The Study of Islamic Philosophy

An article (by Ibrahim Bayyumi Madkour) discussing the roots of Muslim philosophy, its contribution and depth, and how it has been regarded in the west.
http://www.al-islam.org/al-tawhid/study-philosophy.htm

Reconciling Transcendence and Existence

A collection of essays, articles and reviews by Parvez Mansoor on Islam, modernity and the human condition.
http://pmanzoor.info/

Seyyed Hossein Nasr : Science and Civilization in Islam.

An article exploring the philosophical and historical differences between western and Islamic concepts of science.
http://www.fordham.edu/halsall/med/nasr.html