I'm looking for suggestions/examples of tools or APIs that enable the mapping of large amounts of time series data into an intensity map.
The data includes dimensions for country, series, and year. Here's an example http://spreadsheets.google.com/ccc?key=t9ZwziZAgy768ZTXDEg8Maw&authkey=CPn0pdoH&hl=en_GB&ui=1
UUorld is a good choice if you want to create videos that show data changing over time. They're heavy on the 3-D, but I found some examples of what appear to be 2-D intensity maps in the gallery. The trial version is free and does not expire.
For static images, I love indiemapper. It's very simple to use and has beautiful color palettes and typography options. It also has 16 different map projections, if you're into that. The free trial is 30 days.
The caveat with these (and other mapping software) is that you may have to convert your data into a certain format, depending on what it is now. For example, indiemapper takes shapefiles, KML, and GPX as input.