Baseball Prospectus also has a great version of WAR but they call theirs WARP.
All three versions of WAR are different. I would not say one has proven to be better than the others by any means. Each one of them has its pros and cons. For example, Fangraphs WAR has the better defensive component, but B-R WAR uses more accurate adjustments for park factors and interleague play.
Here is a chart comparing the difference of the three major WAR systems: CHART
One other interesting comment is that for most players their fWAR is usually higher than their bWAR which is higher than their WARP. If you add up all the WAR scores for all players in the league in 2012 the fWAR total is 691, the bWAR total is 517 and the WARP total is 433. (see WAR Index
) This means that it is easier to earn a point of fWAR than a point of the other WAR scores.
Each of these websites is constantly tinkering with their formulas. WAR is an evolving concept. I imagine it will be a number of years yet before any sort of consensus is reached on the best way to distill a player's contributions on a ballfield into one simple number.