Are you staying overnight on the way, or driving through? The answers might be different depending on your answer to that question. If you're driving through, you're probably limited to 1 or 2 stops?
Tomar, Batalha, and Alcobaca are all fantastic, each with great historical attractions. Unless there's something going on in Fatima, or you are pulled there, it's really just a big (huge!) empty square. Obidos is an adorable town that is pretty touristy, but it can be easily seen in an afternoon. We also went to the water (Nazare), which was gorgeous- felt very different than other places we saw.
I don't think you can go wrong- it's a lovely drive, and lots of possibilities for great stops!
Robert in Montreal