Rather than duplicating what can be found on other websites, we've listed some Bible study tools here, and good places to find and utilize them. If you find others that might be helpful please let us know.
Search the Bible
With the ability to search multiple translations, Bible Gateway is a very useful online tool.
With the catchphrase of "The Sword of the Lord With an Electronic Edge," e-Sword is a desktop application with free downloads of multiple translations, and the ability to purchase many more, in several different languages. Also available, mostly for free, are concordances and commentaries. An amazing tool for Bible study.
Bible Contradictions answered
All Christians have had people challenge us at one time or another with seeming contradictions in the Bible. An important part of apologetics (defense of God's Word, not apologizing for it) is knowing how to answer that. It can also help keep the seed of doubt from creeping in. This website lists 143 common contradiction accusations and how to answer them. Be sure and read the intro to the list also.
Strong's Concordance with Hebrew and Greek Lexicon
Eliyah.com has several different resources, including the Strong's Concordance with Hebrew and Greek Lexicon. The Strong's Concordance takes the King James Bible and breaks it down by word. For example you could look for the word "boat" and you would see every verse in the Bible where that word appears. This is particurally useful if you don't know an entire passage and are wanting to look it up. Next to each word is a number that relates to either a Hebrew word (if Old Testament) or Greek word (if New Testament). You can look those up in the lexicon to see the Hebrew or Greek word the English word was translated from.
Bible Study Tools.com has many study tools, including a section that has many Bible commentaries available for you to search. The site states "Written by well-known and popular theologians, Bible commentaries aid in the study of Scripture by providing explanation and interpretation of Biblical text. Whether you are just beginning to read Scripture or have been studying the Bible daily, commentaries offer greater understanding with background information on authorship, history, setting, and theme of the Gospel."
Commentary Critical and Explanatory on the Whole Bible by Jamieson, Fausset and Brown
The Treasury of David by Charles H. Spurgeon
Geneva Study Bible
John Darby's Synopsis of the New Testament
John Gill's Exposition of the Bible
Matthew Henry's Commentary on the Whole Bible
People's New Testament
Robertson's Word Pictures of the New Testament by A. T. Robertson
Scofield Reference Notes by C. I. Scofield
The Fourfold Gospel by J. W. McGarvey and Philip Y. Pendleton
Bible Sprout is an evangelical website focused on providing the best information about Christianity and providing users the ability to go deeper in their faith. There's lots of information here on everything from Who Jesus is to How To Pray. Their goal is for Bible Sprout users to have answers to the questions the world will ask them, helping people evolve their faith.