The newest issue of Nature has a list of the fifteen "examples published by Nature over the past decade or so to illustrate the breadth, depth and power of evolutionary thinking." You almost can't blame them for missing some really, really important ones, since they were published in other journals. I am specifically thinking of evolutionary novelties evolving in bacteria and lizards.
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, which reported on the observation of a key evolutionary adaptation appearing by mutation in E. coli, namely the ability to metabolize citrate.
Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource, about a Croatian lizard species, which in about 30 years changed its morphology significantly to adapt to a new environment.
Both of these are studies are gigantic break-throughs, but I suppose you can't blame Nature for not including studies reported in PNAS.
Here's Nature's list:
Gems from the fossil record
1 Land-living ancestors of whales
2 From water to land
3 The origin of feathers
4 The evolutionary history of teeth
5 The origin of the vertebrate skeleton
Gems from habitats
6 Natural selection in speciation
7 Natural selection in lizards
8 A case of co-evolution
9 Differential dispersal in wild birds
10 Selective survival in wild guppies
11 Evolutionary history matters
Gems from molecular processes
12 Darwin’s Galapagos finches
13 Microevolution meets macroevolution
14 Toxin resistance in snakes and clams
15 Variation versus stability
Camponotus: A Sugary High
18 hours ago in Catalogue of Organisms