I highly recommend this post on ID the Future. It provides a great discussion of the relationship between science and the unobservable, an oft cited argument against ID, which demonstrates that Evolutionary theory actually makes appeals to unobservable events and beings as well. The post lists 3 other parts of the series, which are also fairly good, especially 3 and 2 in that order.
The discussion of the unobservable reminded me of the recent refutation of Dark Matter. From what I understand, it sounds like astronomers applied a certain mathematical model to the universe which indicated that more matter existed than they had previously observed. This matter today remains unobserved, but numerous Dark Matter theories have sprung up to explain the descrepancy between the observed mass and the theoretical mass indicated by the model.
The funny part, which is the primary focus of the paper by Cooperstock and Tieu, is that the model was based on the assumption that Newtonian physics, particularly relating to gravity was a good enough approximation and an the fact that it was also an easier conceptual model to deal with. Cooperstock and Tieu adjusted the model to use General Relativities gravity model and poof, the dark matter (that is, the descrepancy between observed matter and theoretical matter) vanished.