First, I second Fast Food Nation as an excellent read; its not polemic, or extreme, just realist and graphic, and that's more than plenty to reinforce or start some good eating habits!
Second, I have seen FOOD Inc; at last year's TIFF. I recommend it highly. Its not too long, it tells its story well, and while I'll grant you it was playing to crowd into the subject matter, the film got a standing O at the TIFF screening I was at, and it was a sell-out.
It deals with a variety of issues; from humanely-raised and killed chicken vs Intensive Livestock operations; shows you how ground chicken is literally bleached, (that was stomach turning).......
Also covers Monsanto, as you'd expect, and they're efforts to harass farmers, seed collectors etc. into leaving the business or becoming Monsanto customers.
And delves into the issue of glucose-fructose as a sweetner vs. sugar or honey and the implications thereof.
Again, very good film.
Haven't seen Food Matters.