Starling Marte lost to Carlos Gonzalez for the Gold Glove in left field, Andrew McCutchen to Carlos Gomez for center, and Russell Martin to Yadier Molina at catcher. P2 has some analysis here.
Marte's snub was obviously the standard Gold Glove travesty. Gonzalez missed a third of the year and trailed Marte badly in the defensive metrics, but he hit 26 homers. Gomez was much more understandable, as he had a phenomenal year defensively and, more importantly, he also had a big year at the plate. As Tim notes, you can make a strong argument for Martin, but the media's mindless, drooling reverence for anything that resembles this has elevated Molina's reputation to Jeteresque levels, albeit with far stronger basis. I suppose we should be thankful that McCutchen didn't lose his spot in the finals to Jon Jay.