This Europe Map Archive from the University of Oregon contains clear, color maps, some of them interactive. Particularly useful for the New Testament student are The Jewish Diaspora in the First Century and the Spread of Christianity map, the latter requiring Shockwave plug-in.
The Barrington Atlas is a reference work of the ancient Greeks and Romans, the lands they penetrated, and the peoples and cultures they encountered in Europe, North Africa and Western Asia.
Seven maps of the ancient near east (Egypt, Sudan, The Levant, Syria, Turkey, Iraq, and Iran), locating primary archaeological sites, modern cities, and river courses set against a plain background. At the Oriental Institute, University of Chicago.