Wow. Rory isn't exactly the most brilliant companions that we've ever met, but i think that he is the most perceptive.
In the Eleventh uur he already proved himself to be observant when noticing the comatose patients out and about.
Then even before he was introduced to the TARDIS he did his research. Even if he's not clever on his own he knows how to find his info.
But finally he showed his quality when he exposed the Doctor. Davros did it at during Journeys End, but Rory was so much meer blunt and got down to the core of it. Its not that the Doctor makes weapons out of people, he makes people want to impress him! The Doctor makes people a danger to themselves. and Rory nailed it! He saw right through the Doctor. And I love him for that.