It depends, but the vast majority seem to take your most recent score (of the schools I looked at).
Some take your best subsection (like GWU) and some take average scores.
Take the time to research this because it may actually be important in deciding where you apply. I know a few people who took the MCAT once without studying much, got in the low 20s, and then took it again and got in the 30s. If they applied to a school that averages, that could be a problem.