I haven't seen this answered anywhere, but does something or some software exist to fine tune manual (!!) focus confirmation (the dot at the bottom left) to more accurately represent focus? If I have the triangle pointed rightward I know I'm in focus, rather than seeing just the "dot", and it's really putting me off. Would love to fix this, and I'm not afraid to use 3rd party software to get it done.
Based on discussion in the comments above, where it is experimentally verified that autofocus microadjust can move the automatically-found focus point back and forth from the point identified as in-focus for the manual focus confirmation — I think your theory is right and the adjustment is just applied as an offset to auto-focus. This is somewhat surprising, because as Kamen notes in another answer, it's just using the same autofocus sensors. Possibly a firmware update could change this, but I wouldn't hold my breath.
What I bet you can do, though, is send your camera and lenses to Nikon and ask Nikon to calibrate the manual focus confirmation for you — they can make adjustments that aren't available to end-users (possibly including physical shims, even).
The procedure should be quite similar to the one for calibrating with autofocus lenses (since the camera still uses the AF sensors for confirming manual focus), the only difference being that you must manually focus the lens during the test when you would otherwise be using autofocus.
You need to use the Setup -> AF Fine-Tune menu.
First there's a quick-and-dirty one that you can try. Shoot a portrait like you normally would and look for focus confirmation. Take 3-4 shots using a wide open aperture (so that the DoF is as small as possible) and look at them. If the actual focus is consistently closer than it should be (front focus), you should apply a positive value. Respectively if it's farther than it should be (back focus), apply a negative value. Start with +10 (or -10 respectively) and work from there until you have correct focus.
The more involved and time-consuming method is by using a test chart like the one linked on this page or a ready-made one like LensCal. Avoid other ones that you can find that require you to place the chart at a 45-degree angle - this introduces an inconsistency. Place the chart on a stationary horizontal surface. Place the camera either on the same surface or on a tripod so that the focal axis is on the same height as the centre of the chart. Some people recommend that the object distance should be 20 times the focal length of the lens, others say it should be its minimum focus distance, I tend to fall somewhere in between. Focus as you would and look for the confirmation dot. Take the shot and look at it. If the actual focus is closer to you, apply a positive AF Fine-Tune value (and vice versa), then de-focus the lens and repeat the procedure until you have the zero in focus.
This is specific to every body-lens combo due to manufacturing tolerances.
From my experience this should be done for every different source of light that you might be using - e.g. you may have perfect focus in daylight, but issues in artificial light.
Hope that this helps.
The only way you will get good results with a manual focus lens is to use Live View, or you can buy a third party focusing screen. I only use manual focus Zeiss lenes and it can be somewhat frustrating at times....Also shoot off a tripod if you can.