For the very first filter (i.e. Keep Yes/No) I use ViewNX2, because it allows easily to spot images that are not up to your standard or which don't tell the story you thought they would do.
For the standard processing (cropping, white balance, etc.) and cataloguing it has been over the recent years Aperture (I appreciate the non-destructive editing, as well as the occasionally the versioning), which still holds my complete catalogue. With Apple's recent announcement I might move over to Lightroom 5, however I have still to figure out how to migrate my complete database and what the pay-offs are, before taking that step.
More recently added DxO as a pre-processing step.
For advanced post-processing (cloning, etc.) I am using the softwares provided by McPhun.
Probably I could combine some of the operations above by using PS, but I definitely don't like the way of licencing by Abobe.