Lost in the shuffle

I've been following the controversy over Intelligent Design and its proponents with great interest. The latest court case out of Dover, Pa. has been widely publicized and I think the judge in this case made a very valid argument as to why ID has no place in a science class. A broader question, and one I've heard no discussion about, is which lines of inquiry or, more specifically, which critical analyses of evolution theory actually HAVE been made over the last, say, 25 years, that have been based on real evidence, i.e. the archeological/anthropological/geologic record? What analysis of specific elements within evolution theory, for example, change in gene frequency, have been debated and what was the nature of that debate or that analysis? I ask this because it seems to me that regardless of the fact that the media have pitched the ID v. evolution story as a conflict between belief and reason, the--pardon the pun--evolution of Darwin's theory has been picked apart over the years by scientists themselves and has held up quite well. However, it's my guess, and I'm not a scientist so this is a hunch based on a variety of reading, that there are parts of Darwin's theory that don't fit the evidence. Am I on the right track or is evolutionary theory just so rock solid that there are absolutely no holes to poke into it?