What runway is used in a 90 degree crosswind?
One would basically follow the same guidance as if the winds were calm:  If the field is tower controlled the controllers will pick a runway.  There may be a primary runway direction preferred in these circumstances for noise abatement, traffic routing, (i.e. Instrument Approach or Standard Instrument Departure procedures favoring one runway over another) or other considerations, otherwise they might consider whether the winds are forecast to shift to favor one or the other and base their decision on that.

At a non-tower controlled airport pilots would be expected to monitor a common traffic frequency and follow what others are doing.  And if you are the first or only person there, lucky you... take your pick!