The Athenian Agora Excavations : Relatively new site with updates on excavations and a tour of the museum and agora using the Quicktime plugin.  Designed for easy use by public.
The Nemea Valley Archaeological Project : Sponsored by Bryn Mawr College with fieldwork done by the American School of Classical Studies at Athens. The site is at the University of Michigan.
The Ohio State University Excavations at Isthmia :
University of Chicago Excavations at Isthmia   (also, Computer Generated Reconstructions of the Sanctuary of Poseidon    )
Corinth Computer Project   :
Kenchreai Excavations   :
Pylos Regional Archaeological Project : Located at the University of Michigan.
Minnesota Archaeological Researches in the Western Peloponnese :
Eleusis Archaeological Project : Located at the University of Manitoba. *

Archaeology on the Net : Home to the Archaeology on the Net Web Ring (which I am a member of), they also have numerous archaeology and ancient history links, though their Greek sites are still a little sparse. They also are the home of the Golden Trowel Award for the best archaeology sites on the web. !
Digging up the Past : Australian journal (Diggings) and magazine (Archaeological Diggings) bringing Mediterranean archaeology to a wider audience. *!
The Mining Company - Archaeology - Greece : A great idea. List of sites in Greece in text format with the links to URL's related to those sites and a short description.  Hopefully more pages will pop up here. Also has links to Greek archaeologists' personal and professional sites.  !
Anthropology in the News : Anthropology, but also Archaeological news stories constantly updated at Texas A&M.
Yesterday Today's Archaeology News Search : Archaeological news by NewsNow in the UK. Searches mainly British sources.

Other Academic Computer Projects on Greece

Metis : Terrific for getting a good idea of the archaeological sites of Greece if you have never been there.  If you have, you can just browse around places you have visited and reminisce.  Great idea.
Dr. J's Illustrated Sites of Greece : If you are looking for pictures of archaeological sites in Greece, look no further than Dr. J.  She has got plenty online now, and lots more on the way.
The Prehistoric Archaeology of the Aegean : Absolutely wonderful site.  Don't miss this one if you have any interest in Bronze Age Greece.  Too bad there are not more sites like this one!!!
Ancient City of Athens : Plenty of good photos of ancient sites in Athens. Been around a while too.
Computer reconstruction of the Palace of Nestor : online at the Antikensammlung Erlangen Internet Archive.
The Temple of Zeus : A VRML representation of the Temple of Zeus at Olympia. *
A Reconstruction of the Acropolis : A computer recreation of the Acropolis and south slope by ARCHIGRAF students at the Kyoto (Japan) Institute of Technology.  Not too bad for first year students. *
The Theater at Messene : A VR model of the theater at Messene has been recreated by the Department of Engineering at the University of Ferrara, to explore the application of virtual acoustics to the study of ancient theatres.  *
Recreating the Theater of Dionysus in Athens : Didaskalia site, uses images of a 3-D reconstruction of the Theater instead of the usual boring pictures (also has an introduction to Ancient Greek Theater).  *
Computer reconstruction of a "housemodel" : online at the Antikensammlung Erlangen Internet Archive (in German). *

Ancient Sites : Walking Tour of the Acropolis :  As the Acropolis might have looked like in Classical Athens.
The Parthenon Marbles : A little more of a political edge here, but a good place to go for info on the marbles.*
Virtual Tour of Acropolis : Could be better, but it's ok. Text and a few pictures. *
Die Bildergalerie (Photographs Taken of the Buildings on the Acropolis between 1860 and today) : A great source of big old photos.  (They've got a wonderful museum also!). *
Late Roman Delphi : A short tour through an often neglected period of the site's history. *
Climbing the Acropolis : Part of the Traveling Classroom site, this URL has a good narrative, but some really awful photos.

Hellenic Ministry of Culture : Has an amazing number of sites and museums linked to and described here. Top notch. Be sure and look at their cultural map of Greece.*
Griechenland : A wonderful site in German that has an excellent overall design. The best part, and you don't have to know German to appreciate this, is the amazing panoramic views.  Make sure you have the Quicktime plug-in and download these views. It's the next best thing to being there. *
Timeline of Greek History - HellasNet: A good reference if you don't have Bury & Meiggs handy.  Really a great resource to have online.
Mining Company: Greece : This is absolutely THE place to start looking for information on your vacation to Greece. They've devoted some time to this section and it shows.  There are links and articles here to provide you with types of information I haven't even begun to dream of.  Unfortunately they've dumped their main  'Travelogues' section which was quite helpful. At least they have kept the one for Greece. Thanks to deTraci Regula!!
Headline News of Greece - Phantis : Articles compiled from major resources each day.  Probably the best way to get up to date Greek news from a variety of sources!
Liens Grece : (In French) This site has a number of links in many languages.  It concentrates on archaeological, cultural, and travel sites and has some hard to find sites in French and German linked here.  !*
Maps of Greece from Earthrise : Photos taken from the U.S. space shuttles of Greece. Greek entry is always changing so you may have to start out at their main site and look for photos of Greece that way.
Georama : Strange site. Terrific graphics, really superb.  Not that many total images though and little content, but maybe this will change. It has some great info on the theaters of Greece though. *
The Shrine of the Modern Greek Language : It really will help...honest
Greek - Turkish Friendship Page : Has got the right idea. Constantly updated.
Hellenic Ministry of Foreign Affairs: Pretty cool. Check out the relations between Greece and your country.
Medea, the Musical - Links to Ancient Greek Sites: Most of the best sites to get you started. Regularly updated too!
Greece Around the World : An ambitious site with it's own info on each of the major Greek regions (and lots of nice photos), but still has a long way to go.
Images from Greece : Need I say more?
Selected Sights from Athens from Delphi and the Peloponnese : Lots of good pictures and some maps, but very little text to go along with them.
Theatro : Beautiful graphics and what looks like a lot of information on the ancient Greek theater, but I think they had to take some pages down because they don't have the space right now to include everything on their server.  Check back on this site later. *
National Geographic Traveler Magazine : Great look. Hope they can get more articles and options.

The Classics Pages : Over 500 pages (Yes, that's right. Over 500.) dealing with classical sites, mythology, interactive games, links for Latin teachers, ancient technology, individual authors and more! *!
Cambridge Schools Classics Project : Online home to one of the most popular Latin textbooks around.  Student and teacher sections.  Also has links to "The Top Twenty-One Classics Websites." *!

Mostly Links (not that there is anything wrong with that!)
Cambridge University Links to Classics Resources : One of the site suppliers for the Argos search engine.  Not many, but all the good ones are here. Also updated regularly. *!
Victoria University at Wellington : A medium sized list of specifically Greek sites with a bit of a New Zealand tilt.  *!
Bibliotheca Classica Selecta - Specialty links : (In French) A large number of well organized links dealing with all things classical.  Very good descriptions are given with each link. *!