Bible Gateway - a great site with stacks of different versions of the bible. They also have some commentaries. I have set up chrome to search for passages via their omni bar by typing ESV
and a passage or NIV and a passage.
Blue Letter Bible - I don't use this site much, but it is a good tool to do some word studies on and you can find resources on a verse by verse basis.
e-Sword - This isn't really an online site, but it is a cool tool to download. It has stacks of resources that you can download including maps, commentaries, dictionaries, books etc. It also has a section for you to write notes on passages.
YouVersion - I kinda like the idea of this site, but like most social sites there is a lot of noise. This has an online bible and allows you to see other people's comments on a passage. It is kinda like an open source bible commentary, but unlike a wiki, you fortunately can not edit other people's notes, but like a wiki, it can be touch and go sometimes.
Online Bible Study Tools - Someone posted on my blog about this site. I haven't really ultalised everything on this site, but there is lots of things here to keep you busy.
Skeptics Annotated Bible - This might seem like a strange link to have, but I find it useful. It has an online bible with skeptical notes in the side. Some comments are quite ignorant of context of the passage or of the culture, but sometimes they do have some challenging comments that do need answers.
The Resurgence Greek Project - This has an online greek bible and is good for word studies like the blue letter bible, only I like this interface a little better.
The Resurgence - This has a lot of good resources on it, from links to sermons that happened a week ago, to old school authors like Calvin, Edwards and Owen.
Desiring God - Pretty much everything John Piper has ever written or said since becoming a minister. They also post all their conferences that they host online.
Mars Hill Church - This is Mark Driscoll's church and they post their resources online for free.
Centre for Public Christianity - Australian site with mostly content from John Dickson and Greg Clark. I bloged about this site here.
The Gospel Coalition - A conference that happens every two years that is headed up by Don Carson and Tim Keller. Their website also has lots of resources and also links to even more (not off of the stuff they link to is free).
Capitol Hill Baptist Church Audio - Mark Devers church audio which is worth listening to.
Sovereign Grace Ministries - A large library of talks and sermons from Sunday services and conferences. I like their New Attitude conference talks as well as talks from C.J. Mahaney.
Resolved Media Volt - I signed up for access to this page, and they haven't spammed me at all. There are links to past Shepherds and Resolved conference talks as well as a stack of sermons from Crossroads ministries
Monergism - This site has a huge stack of online resources and they also link to even more on the web. They also have an mp3 library.
Christian Classic Ethereak Library - This site has stacks of old books online. You can download I think two pdf's for free and then they start charging for pdf's, but you can read anything you want online for free.