I would love to utilize Pride of Baghdad in a lesson or unit. I'm not sure Y: The Last Man or Ex Machina would be suitable for anything, considering their length and price, but Pride is short enough and inexpensive enough. Plus, who doesn't love anthropomorphism? This would be suitable for a lesson on war, or examining personification and anthropomorphism. Vaughan is an amazing writer, though. Ex Machina stands as my favorite graphic novel EVER.
I'm also a huge fan of The Unwritten, but this is pretty R-Rated, with the violence and language. I doubt it would fly in even a high school setting (not in my southern town, anyway). You're right, though. It's ripe with literary references.