Hi Sean,
Thanks for your inquiry. I sure hope some of the atheists can think of some weaknesses in the theory. It would sure help establish their objectivity, don't you agree?
Not a formal list, but some things that come to mind quickly:
1. The theory begs the philosophical question of whether or not we must always seek unguided naturalistic explanations for
everything we observe. I have a number of blog entries on this. My most recent may be useful to start with
here2. The theory is not directly confirmable in the old sense of the scientific method which called for experimentation and direct observation. All of the most controversial elements of the theory are hidden in the distant past and happen so slowly that the theory predicts they won't happen within a thousand of our lifetimes.
3. The theory is infinitely malleable. While it is presented as plausible because given enough time, anything is possible (see #2), the fossil record has been shown by Gould to reveal very fast changes. Dawkins 'saves' Gould by insisting that it is nonetheless gradual, but my point is that whether fast or slow, the evolutionist can say they have a plausible view. In other words, evolution is not falsifiable (see Popper), because it can be adjusted endlessly, and there never comes a point where they'll say "Ah, I guess we were wrong."
Note that the previous points speak as much to the methodology adopted by scientists on this matter as it does the scientific evidence itself.
4. The definition of 'species' is extraordinarily simplified in order to make evolutionary theory plausible. So, when an evolutionist says we've observed new species being formed, it is because they have a hand picked definition of species in mind. When a normal person uses the word species, they think of all of the morphological changes, etc, that drive our comprehension of different 'kinds' of animals.
5. If we are the result of unguided, purely naturalistic processes, how do we know we can trust our senses and our minds? Given evolution, the most assurance we could ever garner is that it produced a scenario that would maximize our ability to survive and reproduce. We have no reason to believe we are really comprehending the world around us anything like as it is- we have only enough reason to believe we comprehend it well enough to survive long enough to make more little copies of ourselves. Thus, at the heart of evolutions stands a massive inconsistency: if it is true, we cannot trust our minds to know that it is true.
6. Even given evolution, the question of how plausible it is 'because anything can happen given enough time' is in doubt. It is customary to propose that with 4.5 billion years to work with (the approximate age of the earth) anything can happen. But according to the fossil record, nearly all of the earth's bauplans (bodyplans) emerged just about 500 million years ago, which of course is far less time. They emerged, completely fully formed as far as the fossil record goes. We must now decide if it is plausible to believe our biological diversity can be accounted for in just about 500 million years. But it is worse than that, because of the famed extinction event (allegedly a meteor strike or something) around 70 million years ago, which gave rise most famously to the mammals. Can our biological diversity be explained in just 70 million years? Only when evolutionists make this argument about plausibility from the time involved they uniformly invoke the 4.5 billion year evolutionary timescale and not the time frame I have just outlined.
7. Many of the 'proofs' of evolution can be handled by other explanations, too. For example, evolutionists routinely cite examples of microevolution at work as support for their theory, and of course microevolution is not disputed. Evolutionists today are keen to point out that macroevolution is just accumulated microevolution, so they are quite confident in their assertion that evolution has been observed, citing cases of microevolution. But microevolution- 'variation within a kind' is also maintained by young earth creationists. So, since both Young Earth Creationists and Macroevolutionists both expect small scale variations within a population, the fact that they occur cannot be construed as evidence for only macroevolution- it would be evidence for both, and therefore useless to cite.
I could go on and on. I personally start and end with #5. Any concept of the world that undermines our epistemology from the beginning must be rejected out of hand. If I must trust my reason to learn about reality but adopt a theory which undermines my reason then the well is poisoned.