With hat tip to Dr. Phil Blosser, I first note Biblia Clerus, courtesy of the Vatican's Congregation for the Clergy. With uncharacteristic hyperbole, Jonathan Prejean calls it the "Best. Website. Ever." What's so great about it is that it brings together many resources that Catholic controversialists on the Web need to have at their fingertips. That includes Denzinger, which I haven't found anywhere else online. (If you have to ask what that is, you probably don't need it; if you don't have to ask, you'll be like a kid in a candy store). The Bible section too is worth paying for, but don't tell that to the Vatican.
The other is the main site for the Greek Orthodox Archdiocese of America. Brandon Watson of Siris calls it "hands down, the best religious website I've ever come across." From an aesthetic standpoint, I must agree. Whoever they engaged to build and maintain that site deserves more than they're probably getting. It has plenty of resources for non-Orthodox too.