Concerning toning my first step usually is to set the whitepoint and blackpoint in a way that the histogram is spread over the whole range. In photoshop I use the levels tool, In LR the Whites and Blacks sliders - taking care not to clip.
Second step usually is adjusting highlights and shadows or - if in photoshop - I use the curves tool.
Third step usually is local adjustments and there is a whole bunch of possibilities. In LR e.g. You have the clarity tool (careful!), the local brushes, the gradations. When I want to do more sophisticated stuff I move to photoshop, creating and adjusting a layer for each feature I want to change locally and then painting it in with a mask. This is the most dangerous part since you easily overcook the image here and destroy the overall natural look. Unsharp mask, soft light layers, blurred layers and layers with differing exposure/contrast settings are my favourite tools here and I paint them in as needed, usually taking care not to make the image look artificial, except I want a gross look.