The Gorn did, that's why Kirk needed that cannon. Also that shapeshifter in ST:VI, when she/he transformed into Kirk, so basically he beat himself then. I don't think Dr. Soran did(ST:Generations)but he came close. Technically Spock didn't beat Kirk in that episode("Amock Time"), McCoy drugged Kirk so it would look like Spock killed him.
Thanks but I was acurely talking in that side of paradise, spock beates him in that story, when he is thrown into a great rage.
nero and the first officer of the narada in the 2009 movie almost beat him, but nero gets called off because spock takes the jelly fish and kirk kills the first officer with his own holstered weapon.