I completed some research a few months back regarding a statistical way to compare baseball teams across eras and developed a concept called the Greatness Number. Studying dozens of baseball metrics, I found OPS, Run Differential and WHIP to have the strongest correlation to winning. You can read the details of my research here and here.
The sample size is small, but I used the Greatness Number to analyze the various clubs in the World Baseball Classic and found Cuba, not the Dominican Republic, to be the best team in the tournament. The Dominican club ranked second, in front of Japan and the United States, while Puerto Rico ranked sixth.
Full rankings from the 2013 World Baseball Classic are below.
The Greatness Number formula: (0.503+(OPS*0.097)+(RD*0.006)+(WHIP*-0.053)).
Using the same formula, I reviewed the statistics from the two previous tournaments and found the 2006 Japan team to have been the best in World Baseball Classic history.
Delving deeper, I averaged the Greatness Number's of every team over the past three tournaments and found the figure for 2013 was the closest to .500, meaning disparity between clubs has lessened since 2006.
2013 Average: .491 | 2009 Average: .487 | 2006 Average: .489
For those wondering, the 2013 United States club ranked behind the 2006 team but ahead of the 2009 team.
From a global perspective, China has yet to advance past the first-round of pool play, yet their club has improved significantly each year, from .232 in 2006 to .381 in 2013.