Oops, sent my reply to Wikitech first, I hope the discussion does not fork :)
There is a Historical Event Markup and Linking Project
http://heml.mta.ca/heml-cocoon/
They try to address issues mentioned here. There is demo of an animated map there as well.
They choose SVG as the medium which seems a good choice. I know there are (were ?) problems with SVG viewing on Mozilla, but that will be fixed, I'm sure.
Erik Zachte