I don't really consider this a Big Deal, but if you're applying for a job that involves regularly wearing tailored clothes, showing up with the bottom button buttoned might be the tiebreaker that keeps you from getting the job. It really makes you look like a rube.
As for whether to button the top button on a 3-button suit, it depends on my mood and the cut of the jacket. I have some on which I normally button it, but today I'm wearing an Armani Collezioni jacket that I think looks better with just the middle button secured.