I like the Fielding Bible stats. But it's worth noting that different advanced fielding metrics can produce somewhat different results for various players. The Hardball Times revised zone rating (RZR) is one of the more popular defensive stats. According to RZR, Miguel Tjeada was the best starting defensive shortstop in the NL this year.

RZR SS

Carlos Lee was the 2d worst LFer, defensively, according to RZR.
RZR LF

If Matsui had qualified, he would have been the second worst 2d baseman, defensively, in the NL according to RZR. Watching Matsui, you can tell he is a good defensive 2d baseman, but it seemed to me that the was messed up by his on field/ off field injury issues. Everytime he came back from an injury, he had a flurry of errors. He had too many errors, particularly for someone who couldn't stay on the field. When you have as many errors as he had, you have to stay on the field longer in order to make up for it, in terms of zone rating opportunities.