When all variables are controlled and accounted for, the pay gap vanishes almost entirely (talking only a 1-2% difference or lower).
Even according to the BLS, itself, the difference is only ~5%; Obama and other's so called "88 cents to every $1" argument only arises when you compare every single job women hold vs every single job men hold; it's a blatant misuses of statistics and a horrendous use of political manipulation/bandwagonning to get support.
There's been numerous studies on the differences, and they generally find that aside from the whole baby thing, men tend to engage in riskier work, work longer hours, are willing to travel more, and are willing to sacrifice their "passion" for a job that pays well (this is on average).
Women, on average, tend to value stability and flexibility in the work place and typically seek a job they feel as more fulfilling...they'll even typically sacrifice a higher paying job for a lower paying one to get this, if necessary. This is easily demonstrated in men vs women that own their own business. Even in this realm, the men out-earn the women, largely in part because, again, the men tends to work longer hours (and how can you have discrimination when the woman is the owner/ultimate say in a business?)
So really, it's differences in what each sex tends to value (for whatever reason) and not really "discrimination". Again, if you control for all variables; same job, education, general area, years of employment, hours worked, whether they do or do not own the business or not, travel time, etc, and the "pay gap" disappears completely.