No. The Theory of Evolution is not in crisis and I get a bit tired of reading that it is - and never from evolutionary biologists, it seems. For some reason, a select band of philosophers, engineers and computer scientists seem to believe that the whole edifice is being challenged and about to come crashing down - and they're not even all Creationists. (I'm not going to single any out here.) The fact is, the very statement that "The Theory of Evolution is in crisis" portrays a deeply flawed understanding.
There is no such thing as "The Theory of Evolution" unless you are referring to the observed fact that all extant life we know about evolved from a common ancestor (or ancestral population). Ironically, this is the bit of evolutionary theory that is furthest from crisis - it is an observation that is so well supported that it is seems incredibly unlikely to ever be overturned. Science is sometimes over-turned in the light of new evidence - and that possibility always remains - but we believe the things we do for a reason and, as science progresses, we get less wrong and less likely to have a major "paradigm change" or "crisis".
"The Theory of Evolution" cannot be in crisis because it is not a single entity. Like the Trinity, it is three in one. In addition to the factual observation that evolution has happened (and even most Intelligent Design advocates seem to accept this), there is evolutionary theory, yes, but this is a body of theories explaining the mechanisms of evolution, not one single theory. There are a few core ideas - such as gene-centric evolution and inclusive fitness being key for understanding adaptation, and most evolutionary change at the genetic level being selectively neutral - but many of the subtle details are still being worked out and debated. This is not a crisis, it is science. Lastly, there is the historical aspect of evolution - how and why did the particular observed trajectory of evolution happen. This is the hardest one of all to get a good answer about because, just like human history, we will never really know. We can't go back and see. Also like human history, we know there are random factors and rare chance events at play, which makes conclusive answers harder still. It's still interesting to propose and test ideas - just because we cannot know, we can still have plausible and implausible explanations based on the evidence. (A global flood around 6000 years ago is implausible given the data, for example.)
A few different potential causes for crisis have been raised and dispatched over the years but one example that seems to recur is the old chestnut of epigenetics. Epigenetics is interesting but does not threaten evolution as a whole. It does have an impact on how we understand about adaptation and, in particular, the effect of "nature versus nurture" on phenotype (though not always in the direction people imagine). It certainly makes life complicated when you study responses to environmental change. I am yet to be convinced that epigenetics seriously challenges any of the core understanding of how evolution happened, however, just as learnt behavioural traits and any other environmentally-influenced phenotypes have not.
The point is that epigenetic markers are erased and rewritten on very short time-scales, whereas the epigenetic machinery and DNA code recognised by that machinery is not and thus, in line with other features of organismal biology, it is a system that has evolved like any other. (The environment is not reaching out and directly making a modification - it is triggering an epigenetic response, which is encoded by the genome.) It may shift the target of evolution to variation in an epigenetic response rather than direct genetic variation of the trait itself (or, more likely, a combination of the two) but it is not qualitatively any different.
When challenged, those proclaiming a "crisis" sometimes admit exaggeration but argue that biologists are in danger of being complacent about evolution, so it should be challenged in this OTT style. Well, I disagree with this sentiment too and such statements again reveal a deep lack of understanding of what evolutionary theory is to an evolutionary biologist - a tangled, complex web of ideas to be appreciated, examined and torn apart as necessary, not some kind of creed of rule book to rally around. To call "crisis" an exaggeration is an understatement of staggering proportions. To accuse biologists of being complacent is just wrong.
As a "front-line" evolutionary biologist, trying to keep up with all the data coming through from projects like ENCODE, I can assure you that we are not "complacent" about any aspect of evolutionary theory. (Except, possibly, the fact that evolution happened.) No good scientist is ever complacent. Doubt and criticism are our core over-riding principles. What we are - and rightly so - is cautious. Great claims need great evidence. New ideas also need to fit with all the existing data as well as the exciting new stuff. For this reason, Jerry Coyne is entirely and absolutely right to explain all these things within a gene-centred framework and that framework still works (as long as you understand what is meant by "gene" in that context).
Finally, when a fantastic new discovery is tested, double-tested and validated, it is accepted and becomes part of the joyous "poetry of reality" as Dawkins put it. Even here, there is no crisis. Evolutionary theory moves on but, like all good science, it does so slowly and carefully, not in a series of knee-jerk paradigm shifts that ignore the fact that we have our current understanding for a reason - and that reason is past experiments and past data that still need explaining under any new framework.