Online Bible with every English AND Greek/Hebrew word indexed at the Blue Letter Bible
Free, non-copyrighted Bible at www.ebible.org
Bible Foundation e-text library
There was a morphological UBS Greek New Testament (i.e. every single word parsed) in gzip format at funet (though that has now disappeared). Pretty well the same stuff (with a few corrections) is in the chapter-by-chapter UBS Greek New Testament with parsing on this site.
Lots of downloadable Greek New Testaments at Vincent Broman's Home Page
TC: A Journal of Textual Criticism
All sorts of good introductory stuff on the biblical texts at David Washburn's Home Page
Another good page, especially with examples of how errors in transmission crept into the New Testament, is the Interpreting Ancient Manuscripts Web
And a staggering amount of Biblical resources at Resource Pages for Biblical Studies
And many more useful links at Penn State's Internet Resources for the Study of Judaism and Christianity (and Islam)
Find the dictionary you're looking for at yourdictionary.com
CCEL (Christian Classics Ethereal Library) has an absolutely huge list of Christian Classics online. You can buy the site contents on CDROM too!
The Early Church On-Line Encyclopedia (ECOLE) (Link was dead last time I tried, but Google is still indexing it). When complete, ECOLE will be a complete online encyclopedia of church history up to the Reformation. Includes both primary documents and modern commentary. It is still very incomplete, however.
The Internet Medieval Sourcebook is a rich source on medieval (and other) history.
Noncanonical documents is an interesting list of early Christian literature. It doesn't seem to overlap much with CCEL.
biblestudytools.net contains a number of searchable books. Most of these are public domain, but a recent noteworthy addition is Baker's Evangelical Dictionary of Biblical Theology. (So we wait in hope for Baker's Evangelical Dictionary of Theology).
Jamieson, Fausset and Brown's (1871) Commentary Critical and Explanatory on the Whole Bible (part of CCEL) is quite in-depth and useful despite its old date. (Unfortunately it's only divided up by books, so the longer ones take a while to download).
Good introductions/backgrounds to books, and a bit of commentary, is at Bible Studies Foundation.
World Wide Study Bible (part of CCEL) is a pottered collection - mostly sermons on particular texts, rather than an actual Bible commentary. Still, there's sure to be useful stuff there.
Easton's 1897 Bible Dictionary (part of CCEL) covers a wide range of topics, but doesn't seem to have the depth or the quality of the modern Bible Dictionaries you can buy. But the very fact that it is online makes it useful.
Nave's Topical Bible. Nominate a topic and it gives an annotated list of Scripture references.
The Development of the New Testament Canon
Denver (Seminary) Journal has pages containing brief reviews of commantaries, dictionaries and other bible study stuff in its Annotated Old Testament Bibliography and Annotated New Testament Bibliography