Can you create a 'Smart PDF' using Eagle?
I don't think you can do it out of the gate. You may have some luck finding a cam file that does what you need. Some quick googling turned up this:

http://www.eaglecentral.ca/forums/index.php?t=msg&amp;th=31067&amp;goto=107442&amp;54b96c1ce9985e9d6fb9afcd2c81a408/