Ephesians 4 Group - They offer free Bible software! 

Apologetics 

Alpha & Omega Ministries - The ministry of James R. White. 
Center for Reformed Theology and Apologetics  
Christian Apologetics and Research Ministry  
Christian Research and Evangelism  
Christian Resources - The ministry of William Webster  

Creeds, Confessions, and Catechisms 

The Belgic Confession  
The Canons of Dort  
The Heidelberg Catechism  
Westminster Confession of Faith  
The Westminster Shorter Catechism  

Eschatology 

Folks, It's Not That Bad!  
American Vision  
Chalcedon Foundation - Articles from a Reformed/Reconstructionist perspective.  
The Covenantal Kingdom  
WordMP3.com  

Theology 

Abate Not - Reformed Christian and Reformation Resources  
Alliance of Confessing Evangelicals - For a modern Reformation.   
Calvinist Worldview 
Center for Reformed Theology and Apologetics  
A Puritans Mind  
Fire and Ice: Puritan and Reformed Writings  
Hall of Church History  
Ligonier Ministries - The ministry of R.C. Sproul.   
Modern Reformation Society  
The Mountain Retreat Center  
Reformation Ink - Many good articles from the Reformers!  
Reformed Reader - A Reformed Baptist site with many resources.  
The Reformed Theology Source  
TheoCenTriC: It's All About God!  

Magazines and Periodicals 

Credenda Agenda - Bi-monthly magazine on theology & culture! 
Modern Reformation