Hierarchies in NP (under the assumption that P != NP) Assuming that P != NP, I believe it has been shown that there are problems which are not in P and not NP-Complete. Graph Isomorphism is conjectured to be such a problem.

Is there any evidence of more such 'layers' in NP? i.e. A hierachy of more than three classes starting at P and culminating in NP, such that each is a proper superset of the other? 

Is it possible that the hierarchy is infinite?
Yes! In fact, there is provably an infinite hierarchy of increasingly harder problems between P and NP-complete under the assumption that P!=NP. This is a direct corollary of the proof of Ladner's Theorem (which established the non-emptiness of NP\P)

Formally, we know that for every set S not in P, there exists S' not in P such that S' is Karp-reducible to S but S is not Cook-reducible to S'. Therefore, if P != NP, then there exists an infinite sequence of sets S1, S2... in NP\P such that Si+1 is Karp-reducible to Si but Si is not Cook-reducible to Si+1.

Admittedly, the overwhelming majority of such problems are highly unnatural in nature.