The Doctor loves jokes; there’s no better tool for annoying his enemies than humour, preferably at their expense. While they try to be their best evil selves, he cracks jokes, taunts them, makes them react impulsively, even irrationally. When people of any species get angry, they make mistakes. It’s a universal constant.
Besides, jokes are funny, and what’s life without a bit of fun? Dead boring, that’s what. Laughter breeds hope, and where there’s hope, anything is possible.
That’s why the Doctor always wins. Not because he’s smarter, although he usually is, but because he knows which buttons to push.