I have created about 100 maps, of varying levels of sophistication, for the Web. The early ones used a proprietary system invented at the Star in 2004, while more recent ones use conventional KML. Some involved boundary sets I created, while others use boundary sets imported from formats intended for print, like .shp files.
At the moment, our most complex maps show about 1,000 census tracts in the Toronto area, each with its own customized popup box.
My ambition is to create maps like this one on the New York Times site, which shows about 6,000 areas and loads very quickly. I am also exploring the storytelling potential of a Google Earth animation presented to the reader as a movie file with voiceover.
Here is a recent video. Mouseover the image below to start:
Here is a screenshot from one recent map: