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.
On a Nikon, [AF fine-tune] is linked to the lense's s/n in the built in CPU, usually you assign the last 2 digits of the lens (from the CPU) to the newly tuned value.
The issue you have with non Nikon lenses (eg Lensbaby, with no CPU) and back focus (which is typical for most Nikon lens/body combo, so go to the minus side) requires a [Default] value adjustment which mean GLOBAL FOR ALL lenses and saved [AF fine-tune] values. That means ALL LENSES will be +/- from what ever you may have done to specific Nikon [AF fine-tune] values.
The reason you need to change the [Default], is that the Nikon body cannot assign a specific +/- value to an item with no CPU. Nor can it get the data you assigned in the [No-CPU lens data] = that is only used for metering. So you cannot assign a non-CPU lens number to the [AF-fine tune] menu.
So, in your case, I would change the [Default] to a (-) or (+) value that you can ascertain using a ruler at a less than ~45 degree angle, and focus in the middle using the [ > o < ] green indicator in the lower left corner of the viewfinder. Keep adjusting the [AF fine-tune] until you get a sharp result for that lens. Make a note of the selected value, and use that corrected value in the [Default] each time you use that specific lens. NOW, YOU MUST RETURN the [Default] value to  when finished, and going to use another lens. A good tool, is Focus Tune by Michael Tapes Design. You will discover that all your Nikon lenses focus at different +/-. The [Default] setting rarely, if ever, needs to be changed, unless the AF system is out of whack, and you are far, on a trip, from a Nikon Repair center. Good Luck, hope this helps, and logically clear. Oh!and make sure you turn on the [AF fine-tune (On/Off] to enable the changes... return to [Off] when finished using that lens.