The Digital Archaeological Atlas of the Holy Land (DAAHL) is an international project that brings together experts in information technology including Geographic Information Systems (GIS) and the archaeology of the Holy Land (modern Israel, Palestine, Jordan, southern Lebanon, Syria and the Sinai Peninsula) to create the first on-line digital atlas of the region.
Eye On Israel offers interactive maps of modern and historical Israel. (Once at the website, click on Atlas to get to the historical maps.)
The Virtual Jewish Library offers lots of maps of Israel and the Middle East–both historical and current. Topics include:
Israel’s Ministry of Foreign Affairs presents Israel’s Story in Maps (both online and downloadable):