Chronological Bible: ESV
Read the Bible chronologically. The first time I read through the Bible in the order everything happened, I learned so much and gained an incredible understanding of the big picture of Scripture. If you've never done it, you should!
Bible Gateway
From this website you can search for scriptures in a number of versions and languages by key words, phrases, or references. I use this website often when I post Scripture on my blog, so then I don't have to worry about typing in the verse accurately.
Treasury of Scripture Knowledge
This is a fantastic online version of a classic reference tool. Basically this is a list of cross references based on particular passages. Simply click on the verse or passage you are studying, and you will find other references to other relevant Scripture.
Bible Commentaries Online
A list of classic Bible commentaries. Sometimes they're hard to understand, but they can be helpful when you're wanting more insight into a passage you are studying.
More Bible Study Resources
This is a page of links for articles and audio on the topic of studying the Bible. Some are not easy to read, but they are helpful.
The rest of this website has a tremendous amount of resources that may be of interest.