I've been reading a little bible lately and also discussed it with believers. This, of course, can be straeneous, but you learn a lot as you go.
The most obvious, and probably the most well-known tool among Atheists is Skeptic's Annotated Bible. It takes you right to the goodies. It has to be said, that sometimes it tends to take a worst case interpretation of verses, so whatever you do, you need to read it in context. But as for showing you the good stuff, and the subjects you need, it is pretty perfect.
Notice that SAB also provides you with links to articles about the subjects at hand, even including apologist rebuttals. You get both sides then, so you can prepare for counterarguments.
Skeptic's Annotated Bible is the King James version, and it is not always the most reliable translation. Therefore, Biblegateway is good because it allows you to easily compare different translations, also non-English. For generally searching the KJV bible, Blue Letter Bible is the most easy to use.
A tool I found today however is a real goodie: Scripturetext.com. You look up a passage at the upper left and you can see different translations below, including Greek and Hebrew if you push those tabs. The real nice part is to hit the Lex tab because you get dictionary definitions of each word in Hebrew/Greek so you can easier see if the translations into English (etc.) could have had different meanings. And you can probably counter the more blunt attempts by apologists to explain away about what the words "really" says.
I now also noticed that Blue Letter Bible has a similar function to Scripturext. When you have a list of bibleverses, you can hit the C tab for Concordance on the left. Then you'll see al the words of a verse, and their Hebrew/Greek counterparts as well as Strong's numbers. Click a number, and you'll get a list of all the places that the same Greek/Hebrew word has been used in the bible.
Here are also two informative sites:
The Rejection of Pascal's Wager. Don't let you scare away by the title, because there's much more than Pascal-bashing. If you read up on the texts on Paul and Jesus and scriptures, you get introduced to a lot of good research, complete with references and all. I'd wish the site had a better structure, but there's a lot to be learned.
Religious Tolerance is also good. It's not an Atheist site, but gives you information about beliefs and theology from a critical and liberal view in addition to providing the conservative view. This can often be illuminating.
Last year I read Who Wrote The Bible by Richard E. Friedman. It's about the Documentary Hypothesis, which says that the five first books in the Bible were not written about Moses, and gives some pretty interesting insights into higher Bible criticism. I don't think anything compares to get the introduction from this book, but even so, here are some OK links on the subject of the Documentary Hypothesis:
Article at University of Pennsylvania website and example using the flood story.
Article at Religious Tolerance.
Well, that's enough research for now!