Updated Resource Map. The small map in the 1980/1983 Greyhawk Guide showing regional resources of the Flanaess is one of my favorites. The LGG updated each nation's resources with new entries like livestock and ship building. A new map with this info is high on my list of DM utility maps.
Battle Maps. This one is also a long term dream of mine. We've all seen the Flanaess map that shows the migrations, but it would be just as interesting and informative to see the direction of various battles and wars. Just hearing about the Battle of Emridy Meadows, the Short War or the Hateful Wars is nice, but where do these forces originate and what direction do they advance or retreat? A simple themed map with arrows can teach players about the conflict faster than a long, boring treatise on the subject.
Ancient Flanaess Maps. Another handy map for history lessons on the fly. What did Eastern Oerik look like 500 years ago? 1000? and so on. I've meddled in making one before but the research of canon often shuts me down. A good example, someone once made an amazing series of maps showing the evolving size of the Great Kingdom of Aerdy. (map to the left) I need to find the link to this map. Also what DM wouldn't like to know what the Flanaess looked like when elves and dwarves held sway? Or ancient Flannae civilizations? There would even be geographical differences, like larger forests or cities that are now ruins. The applications for such maps are unlimited.
Update: Got a link to those historical maps here courtesy of Greyhawk Grognard (thanks Joseph).
Magic Aura Map. This one is extreme so bear with me. It would be daunting to research but fun to see all the magical sites (such as Tovag Baragu and other permanent gates) and ley lines (sites of druids, lost lands, wizards towers, etc) and lingering auras (Dry Steppes, Sea of Dust) present in the Flanaess, all charted on the map somehow in levels of intensity. The utility is that wizards would know which areas to go or avoid in a general arcane knowledge sense.
Monster Hunting Maps. How about a reference map for common D&D monsters for PCs use in game? You could have areas marked where dragons or giants are found and what type. Heck you could even get create and tag owlbears, ogres or otyughs. Anything! Hand that out to hack n slash players and let them pick a destination.
That's all I got for now. Anyone else have some crazy ideas for a Greyhawk themed map?