There have been several reasons floated around for BART's odd (for the US) gauge. These include Southern Pacific demanding a break in gauge to prevent freight competition (looking at BART's system, I consider this one to be urban lore), higher safety for a proposed and never implemented crossing on the Golden Gate Bridge and the designers simply not being aware that such a thing as standard gauge existed.

The most plausible explanation I have found is that BART was intended to be groundbreaking and the template for a new type of transit system, so the designers were given a blank slate. Studies were done during the design phase that defined a car outline of X width for passenger comfort and this in turn influenced a call for a wider gauge, 5'6", which would allow stable, "high" speed operation of this wider car. Note that the gauge is not the only item out of standard for BART, its car outlines are also wider than AAR specifications.

However, BART was not widely emulated. Only Washington DC's system is similar and they opted for standard US gauge. The wide gauge has reportedly been a factor in higher cost (custom ties are needed, for example, as are custom or modified wheelsets and bogies), but in other ways the system has proven quite successful. BART cars are among the most comfortable in terms of seating arrangement that I and others I have spoken too have encountered. And they are inherently more stable with their low slung bodies and wide wheel stance. In theory, the system should be capable of much higher speeds that other transit systems, but seems to be limited by signalling and track structure.

One item often blamed on the gauge is BART's distinctive track whine when in curves. I have never encountered another rail or subway system that sounds quite like it or is as loud. However, it has been pointed out that gauge alone should not cause this. It is perhaps a harmonic that results from the gauge coupled with the wheelbase of the trucks and the long truck center measurement.