http://www.islamic-awareness.org/ (This site contains the most scholarly articles written by any Islamic apologetics website. They focus mostly on refuting the so called historical errors to be found in the Qur'an. They also have excellent articles on historical Christianity.)

http://www.bismikaallahuma.org  (contains some excellent articles, while most of the others are very good. Strongly recommended site)

http://www.muslim-responses.com/ (Contains many useful articles that are written in a very logical and simplified manner for the reader. The articles are written more in an informal way, which makes it entertaining for the reader to digest the information, in contrast to taking a more formal and scholarly approach)

www.islamic-answers.com (this website is being run by brother Karim who has converted to Islam. Allah has blessed brother Karim with the ability to write very excellent articles for the defence of Islam. Karim specialises in refuting arguments especially on the topic of "Women in Islam". I would like to mention that I disagree with brother Karim's stances and opinions on Sufism, although Karim quotes respected Sunni scholars to back up his views, we [call-to-monotheism] do not agree with these views and have also many reliable Sunni scholars that back up our view, we believe the scholars we follow are right on this issue of Sufism, and Allah knows best)

http://theinimitablequran.com/ (provides great arguments regarding the supernatural eloquence of the Qur'an)

http://www.drzakirnaik.com/Features/QAOnIslam/tabid/56/Default.aspx (over 50 most common misconceptions answered by Dr. Zakir Naik)

http://www.load-islam.com/artical_det.php?artical_id=414§ion=wel_islam&subsection=Misconceptions (Contains a big list of Quranic verses and hadith that are most commonly misquoted by Islamophobes and addresses them)

Refuting Shias

http://www.ahlelbayt.com/

http://www.sunnidefense.com/exp/ 

Refuting Sikhs

http://www.islam-sikhism.info

Refuting Popular Islamaphobes

http://loonwatch.com/

Muslim Contributions to Civilization

http://www.muslimheritage.com/topics/default.cfm

http://www.1001inventions.com/index.cfm?fuseaction=main.viewSection&intSectionID=309 

Islamic E-Books (English and Arabic Sites)

http://www.ibnothaimeen.com/all/books/cat_index_317.shtml

http://www.sunna.info/books/

http://www.islambasics.com/

http://www.kalamullah.com/books.html 

http://www.hoor-al-ayn.com/books.html 

http://www.almuflihoon.com/#nogo

http://www.islamebook.com/

http://www.library.mohdy.com/ 

http://www.islamhouse.com/pg/9661/books/1 

http://www.islam-qa.com/index.php?pg=articles&type=1&ln=eng 

http://abdurrahman.org/ebooks.html 

http://www.waqfeya.com/list.php?cat=30

http://haqaonline.com/multimedia/ebooks/

http://www.quranicstudies.com/downcat7.html

http://www.streetdawah.com/books.html

http://www.witness-pioneer.org/vil/Books/

http://www.taimiah.org/books02.asp?pid=1

http://www.sahab.org/books/books.php?cat=0&query=&page=1&type=1

http://saaid.net/book/index.php

http://www.almeshkat.net/books/index.php

http://www.al-eman.com/Islamlib/authalpha.asp