I'd add that it could be argued that Noise Reduction (like Noise Ninja) should be done before sharpening, perhaps best in the demosaic stage, but this is not really and option if we use Lightroom. Would be nice if Adobe would make it possible to use industry strength NR and distorsion and keystoning correction in a parametric workflow.
A good bit of reading on the background of sharpening, masking etc. can be found here.
Look for the tuorial "put a fine edge on your sharpening skills". Even though I don't use the tools this website provides it helped me understand better what sharpening and edge masking was all about.
With regard to my workflow, I just put all sharpening in all intermediate applications (like Noise Ninja, Genuine Fractals....) off, so I only sharpen twice:
Capture sharpening in the lightroom develop mode
Output sharpening for a specific medium/size in Photoshop CS using Photokit Sharpener (allthough I have started to dabble at the Lightroom print output sharpening).
For me this gives the most consistent results I understand best. There might be better ways but I haven't found them yet.