I would say that the most important and, in my opinion as a bioinformatician, the most interesting, evidence for evolution is found in the thousands of whole-genome DNA sequences from a wide array of species obtained in the past 33 years.
If the sequences are compared to each other, cladistic analysis and the principle of maximum parsimony can be used to map out a tree of these sequences. This tree, in virtually every case, matches perfectly with the phylogenic tree of life obtained from the fossil record through comparative homology. I would provide some references for this claim but I'm limited to 2 links, but Google Scholar is an excellent resource.
Darwin had no idea that genes or DNA existed when he wrote "On the Origin of Species", but over 100 years later there is yet another large body of direct, objective evidence for the common descent of life on Earth. People who deny evolution just do not understand that when there is this amount of evidence for a theory, it would take an equal or greater amount of evidence to disprove it, and an explanation as to why the current body of evidence looks correct but isn't. In any real science, there are always controversies and unsolved problems. We have no idea what exactly it is that causes gravity, but no reasonable person doubts that gravity exists.