Some people try to point to the missing links in the fossil record, especially regarding the evolution of the human species, as though this is a flaw in the theory itself. This is not a valid point, in my opinion, because of the overall rarity of fossils. The fossilization process only occurs only certain conditions, the result being that many species that quickly died out or lived in a small area would not be fossilized. Darwin himself commented on this supposed hole in his theory.
I took this straight from wikipedia
Fossilization is an exceptionally rare occurrence, because most components of formerly-living things tend to decompose relatively quickly following death. In order for an organism to be fossilized, the remains normally need to be covered by sediment as soon as possible. However there are exceptions to this, such as if an organism becomes frozen, desiccated, or comes to rest in an anoxic (oxygen-free) environment. There are several different types of fossils and fossilization processes.
Due to the combined effect of taphonomic processes and simple mathematical chance, fossilization tends to favor organisms with hard body parts, those that were widespread, and those that lived for a long time. On the other hand, it is very unusual to find fossils of small, soft bodied, geographically restricted and geologically ephemeral organisms, because of their relative rarity and low likelihood of preservation.
Larger specimens (macrofossils) are more often observed, dug up and displayed, although microscopic remains (microfossils) are actually far more common in the fossil record.
Some casual observers have been perplexed by the rarity of transitional species within the fossil record. The conventional explanation for this rarity was given by Darwin, who stated that "the extreme imperfection of the geological record," combined with the short duration and narrow geographical range of transitional species, made it unlikely that many such fossils would be found. Simply put, the conditions under which fossilization takes place are quite rare; and it is highly unlikely that any given organism will leave behind a fossil.
We are lucky to have the fossil record we do, and there will always be "missing links" (were running out of places to look), but this IS NOT a flaw in the theory.