Bible History Online - includes book studies and commentary on OT Canon and NT Canon, as well as many essays on "the stuff between the lines".
Prof. Ralf Klein's Links - includes links to important sites, exercises, and more.
World Wide Search of the Bible - provides many downloadable essays and commentaries on the Bible - excellent for research.
Encylopedia of the Orient - exactly what the name says, including a helpful link to maps of the orient.
Enter the Bible - An excellent if brief introduction to every book of the Bible and more from Luther Seminary in St. Paul, MN.
Internet Ancient History Sourcebook - not all the links work, but the ones that do have good information!
Jewish Encylopedia - A searchable on-line Jewish encyclopedia. Older, but still quite useful.
Greek New Testament with Search Engine. Several sights are linked to this helpful page from the University of Birmingham.
The Jesus Project. Research on the historical Jesus from a sociological perspective.
Jesus in Early Christian Gospels
Frontline: From Jesus to Christ
Apocalypticism in the Bible. An excellent resource on from Frontline (PBS).
Search several differnt translations/versions of the Bible on Bible Gateway
Ancient Maps sites
The Virtual World Project is not a map site, but you can virtually visit important archaeological sites.
Close to complete set of Biblical maps
Map of Dead Sea Scroll Excavation Area