See this Wall Street Journal article for an interesting take on evolution and Modern Orthodox thought.
In a recent discussion with some of my chevra , we concluded that TRUE science and TRUE religion - since all of the above emanate from the same God - cannot be in any conflict.
However, in the human realm, we don't really understand the ultimate truths of science yet, as we probably only understand Torah or God superficially. One day, there will live a Rambam and an Einstein all wrapped up in the same person who will get to the bottom of both realms. He will discover that when you really comprehend both Torah and science, their only conflict is semantic.
I believe it was R. Sa'adya Gaon who first posited that we will grasp the rational meaning of more and more mitzvoth over time.
Here is an example: most meforshim interpret "Taninim Gedolim" as sea monsters or whales... This is loosely based on Hirsch on Parshat Vo'eira. He asserts, basing himself on the Haftorah, that we can interpret "Tanim" as crocodile and "Taninim g'dolim" as great lizards - dinosaurs. A little bit of archaeology, some flexible etymology, and you can point to dinosaurs within the Torah.
What is definitively true of the Torah well before Darwin is that it describes a creation process progressing from the simple to the complex. Thus, we see the confluence of Torah and Mada as an evolving process - pun most intended.