The indispensable Speculative Catholic points out this TechCentralStation article about Natural Theology, Intelligent Design and Teilhard de Chardin.
Honestly, I don't know as much about de Chardin as I ought to, but the article is worth a quick read. One of the points worth making that the article touches on is that ID (as in the semi-scientific body of thought pushed by the Discovery Institute) differs from many of the great non-naturalistic cosmologies in history in that it doesn't find the creator in the order and nature of the universe but in certain little details.
Given the scope of modern science, I don't think you can prove God's existence using science itself. But if you want to derive evidence for God's creative hand from the physical universe, I think there's more to be found in the fact that the universe has order and operates according to laws than in the bacterial flagellum. This is additionally useful in that a being capable of creating the universe with stable, constant physical laws must of necessity be something like what we call God, while (as the Discovery Institute is eager to point out when trying to get into secular public schools) the designer of the flagellum could just as well have been your average alien playing around with a flagellum-making machine.
Really, though, if you want to find God, I think you need to hearken back to Aquinas and Plato who found God in the existence of ideals. For there to be such a thing as objective good (rather than personal advantage or preference) there must be an ultimate Good, and that Good we refer to as God. Ditto for justice, love, etc. Qualities such as good, justice and love are totally beyond the powers of such fields as modern science to investigate, and so there's no turf war to be fought over whether theology and philosophy are acting in their right place.
Further, it is easily discernible to any person in any place and time that good, justice and love are qualities which exist and have degrees that relate to some absolute. This formula has been persuading people since Plato's time, if not before. The bacterial flagellum is observable only to modern man with modern tools, and by playing in science's sandbox, the ID movement leaves itself open to the possibility that there in fact is a clear evolutionary pathway to the flagellum that evolutionary biologists will one day demonstrate. At that point, any faith built upon the foundation of ID will wash away.