A few times I've experienced that OS X' Mail has just stopped downloading new messages via POP from GMail. I've been all around Google's mail system to try to figure out why Mail and GMail all the sudden won't co-operate anymore. Not having any luck there I began exploring and found a solution:

For the sake of example, my account will be called username@gmail.com

Go to ~/Library/Mail/POP-username@gmail.com@pop.gmail.com

In that folder there is a file called MessageUidsAlreadyDownloaded2. It's an XML file that contains stamps of when what mail downloaded from GMail. Mine was about 45k large. I quit mail, moved this file away (just in case) and started Mail again. And voila! Mail is downloading mail from GMail via POP3S again. And it ...