I don't do anything special - I take my images through Lightroom and Photoshop.
Lately I've been playing around more with Capture One rather than Lightroom since it has dedicated support for Sony and Mamiya and outputs a better final image but they're pretty similar.
As far as tools go, I just use the basic tools of clone, heal, curves, adjustments, etc...
Once in a blue moon I'll use something like Nik but other than that I tend to do everything manually.
You can learn more here: www.vonwong.com/blog/product/vonwongtutorial/