Gaining General Islamic Knowledge
www.islam-qa.com/ (provides very scholarly fatwas and is excellent for Muslims who simply want to increase their knowledge in Islam. However, there is one big distadvantage unfortunately. Many Muslims might find that the scholar doesn't seem to provide the logic and wisdom behind many of the rulings he provides. He only provides scholarly evidence for the correct answer, but does not communicate it in an appropriate way for most people. He assumes that all readers have the 'we hear and we obey' attitude. Even though this is the attitude we Muslims should have, unfortunately not all of us do. Therefore, if you are not that type of Muslim we don't advise you to visit this site. The scholar also holds certain views about Jihad, women and other topics that I personally do not agree with.)
Please note that I don't agree with all the content in the following salafi websites. Some of the websites have serious mistakes in manhaj in terms of how to critique opponents. I am only recommending the below because they have excellent material on Aqeedah.
http://www.islaam.net/main/
http://www.salafipublications.com/sps/sp.cfmsecID=TAW&loadpage=displaysection.cfm
http://www.troid.org/articles/
http://aqeedah.wordpress.com/202/
http://abdurrahman.org
http://www.ahya.org/amm/index.php
http://www.allaahuakbar.in/article.asp
http://www.salafimanhaj.com/
http://www.al-ibaanah.com/support.php?page=articles
http://www.calgaryislam.com/imembers/Sections+index-req-listarticles-secid-5.html
http://www.fatwaislam.com/fis/
http://www.bakkah.net/
http://www.masjiduthaymeen.org/posts/2003/06/21/18.htm
http://www.therighteouspath.com/home/
http://www.almuflihoon.com/
http://thecreedofislam.wordpress.com
Websites that Defend Islam
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.geocities.com/islam_sikhism/
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.ibnothaimeen.com/all/books/cat_index_317.shtml
http://www.ibnothaimeen.com/all/books/cat_index_317.shtml
http://www.sunna.info/books/
http://lsbuislam.co.uk/articlesneeded/
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