This went under the radar, but the new Pentax K-5 IIs is the best DSLR with an APS-C sized sensor. Period.
DxOMark just finished testing the K-5 IIs and graded it #1 in the APS-C sensor category. It is tied for 9th overall, with the same score as the medium-format Pentax 645D, the full-frame Nikon D3s, the full-frame Canon EOS 1Dx, and the full-frame Canon EOS 6D.
The K-5 IIs outperforms the Canon EOS 5D Mark III in every category except for high ISO. It even holds up surprisingly well in most categories to the Nikon D800E, the #1 ranked camera by DxOMark.
It should not surprise anyone that Pentax has the best DSLR with an APS-C sized sensor. The two-year-old K-5 was already the top rated camera in this category. The K-5 IIs is the same camera, just technologically updated and with the anti-aliasing filter removed to increase sharpness.
The Pentax K-5 IIs is $1,300 for the body only, which is an exceptional deal when you consider the cameras that K-5 IIs competes with.