There's plenty of stuff out there about the lack of transitional forms in the development of man, for instance. Archaeological finds have long cast doubt on the traditional Darwinian view of a mechanical progression of species via survival of the fittest. Darwin himself was adamant that natural selection was never meant to be the only mechanism of evolution, although this has pretty much become evolutionist dogma. The range and depth of archaeological evidence against traditional evolutionary theory is rather beyond the scope of a quick comment here for discussion - just run a google search or something. A second point would be the lack of a concept of 'life' in evolutionary theory - nobody can really say how life emerges, although religions obviously try to. A third point would be natural selection's focus on the individual. Weaker or inadequate individuals in a species die out as the stronger survive, and the mutations that create stronger individuals go on to propagate the species. However, this hardly explains the collective activities of some species, such as ants, or flattid bugs, that appear to operate according to some sort of hive mentality where individuals count for less than the group.

A lot more could be said about each of these points but that's as best I can summarise them here. The point is not that evolution is discredited, but that it is open to questioning and refinement as a theory - it shouldn't simply be held as scientific fact.