My belief is that in order to study properly, one needs the right tools and resources. Listed below are website links that I've used or recommend to help when studying our Heavenly Father's word. I've also included my own resources (free to use) for daily prayers, Sabbath (Shabbat), blessings for the new month (Rosh Chodesh), and weekly Psalms (Which can be found in the "Teachings" section). As with anything, do NOT take my word for it, study out scripture and let scripture interpret scripture.
E-Sword is an excellent PC application that has multiple bible versions. The free software (free basic download) includes "Strong's Concordance", bible maps, commentaries, and other resources.
Another excellent companion to have is a Hebrew Lexicon. I personally like the Brown-Driver-Briggs Hebrew and English Lexicon. Amazon usually has a good price on this book.                           
An essential bible for the serious bible scholar is an Interlinear Bible. I personally like to use "The Interlinear Bible" by Jay P. Green. It will have the Hebrew, Greek, and English along with the Strong's Concordance numbers listed above each word. Here is one website that carries this bible:
Listed below is a very good website that will help you understand Jewish thought and Hebraic concepts- includes multiple blessings and an understanding of Shabbat, New Moon, and Feasts of the LORD (YHWH)
Free online bible study tools. Good websites.
Early Christian writings: Didache, etc...
A general understanding of Paleo- Hebrew
Another excellent resource for understanding people, places, religions and other information regarding the bible!