Al-Islam.org
Digital Islamic Library Project - Quran, Duas, Ahadeeth and much more 
Almizan.org
Exegesis of the Qur'an by Allamah Sayyed Muhammad Husayn Tabataba'i
Hujjat.org: Islamic Centre, Stanmore, London, UK
The website of the Khoja Shia Ithna\'asheri Muslim Community of London, Hujjat Islamic Centre, Stanmore
World-Federation.org
Home Page of the World Federation of KSI Muslim Communities
Yildun.com
The Koran - Free Holy Quran software in 17 languages
Ziyarat Maps
Useful Maps for Pilgrims to Makkah & Madinah
Islamic Scholars
Islamic Scholars
Ziyarat.org
Hajj Assistance Committee of North America
Azadari.com
Downloads of Majaalis, etc.
Al-Shia.com
Multilingual Site contains Books, Fiqh, History, Dua, and a very good FAQ
Aqaed.com
Arabic only site containing many articles about Shia idealogy
Duas.org
supplications both for every day and special purposes. audio available
Ashura.com
An Ashura reference site.
Sistani.org
The official website of Grand Ayatullah al-Uzma Seyyid Ali al-Sistani
Quranexplorer.com
Explore the quran by following the arabic text, listening to the Quran or reading the translation - all at the same time!