Best Burger in town at a sit down restaurant is Annies, as Saul points out. Best fast food burger is currently the Pad Burger, but used to be the Buddy Burger.
Fact: The Pad (elite North Topeka fast food burger joint) is owned by the same family that owned Buddy's (previously located on 10th street across from the hospitals), but after Buddy's was taken over by their son (a would-be heavy weight boxing contender, Dangerous Damon Reed), it folded.