Cairo Genizah Collection
This
collection is made up of over a hundred thousand fragments of writings found in the genizah of a synagogue in Cairo. Though they have been scattered
among many collections, they are now being made available online. For
more info see this Wikipedia article.
The University of Manchester has a collection of about 11,000 fragments in the John Rylands Library and available online.
This is a project that aims to bring many of the different Cairo
Genizah collections into a single place. Firefox doesn't work with this
site thus far, so you'll have to use IE 6 or up.
Another attempt at digitizing and making the fragmanets available online.
Bible Codices
This cite has a number of biblical manuscripts available for download in PDF format. The two most notable inclusions are the Leningrad Codex (B19a) and the Aleppo Codex (also available in High Res).
This is one of the earliest versions of the Hebrew Bible available.
Supposed to match the Masorah better than the Lenningrad. It was
complete until most of the Pentatuech was lost in 1947, due to
ant-Jewish riots. The entire codex is made available, and the UI is
very accessible and friendly.
This 4th century manuscript is useful in Septuagint studies. Available online.
Here is collection of a number of manuscripts, including the New
Testament, and Septuagint versions for the Hebrew Bible which include Codex
Sinaiticus and Freer Codex. Also includes many other manuscripts available
there and other sites.
Although not useful for most most biblical scholarship, this is still a fun resource. The entire bible is available online.
Dead Sea Scrolls
Recently it has been announced that the Dead Sea Scrolls will be made available online for free. See this New York Times article.
The entire scroll is online for viewing. Magnification makes it readable, but still less than ideal.
Databases
This online archive contains images from all over the ancient Near
East. Tablets, inscriptions, and some of the Dead Sea Scrolls.