Digital Karnak - University of California at Los Angeles
Egyptology Resources by Nigel Strudwick
Encyclopedia of Egyptology
Digital Atlas of Egyptian Archaeology Michigan State University, class project by 2014 students and thus not likely to be improved
Digital Egypt for Universities by University College London/Petrie Museum of Egyptian Archaeology
An Introduction to the History and Culture of Pharaonic Egypt by André Dollinger
Resources from Memphis Egyptology students - a lot of pdf links

Theban Mapping Project
Mut Precinct, Karnak Brooklyn Museum
The Karnak Great Hypostyle Hall Project Peter Brand, University of Memphis
Nile DeltaMaps by David Rumsey, 1818

Late Pre-Dynastic and Early Dynastic Egypt History, via Inscriptions and Artifacts, with Bibliography by each Pharaoh (some written in Italian, translation is forthcoming). Also good corpus of palettes.

The Virtual Amarna Project Barry Kemp
The Amarna Project official website

Suez Harbor by University of Southampton
MARES Project by University of Exeter; exploring Maritime trade on the Red Sea
Tell el-Dab'aby Manfred Bietak and Irene Forstner-Müller, the Austrian Archaeological Institute in Cairo
Tell el-Farkha (eastern Nile Delta) by the Polish Archaeological Expedition
El Hibeh by UC Berkeley

Photo Archive by René Seindal (site is mostly about Rome, but is adding photos of cities in Egypt)

Ägyptologie Community Ortsliste
Ägyptologie Community Karte

Trismegistos Geo

The Egypt Exploration Society Delta Survey