I just thought that I would add my two cents. Feel free to disagree.
I've come across many product drawings over the years and seen some wild stuff! Generally, GD&T directly reflects the manufacturing process and the actual function of a part, rather than it's physical form. It's used mainly for production parts, but can also be used successfully for one-off parts and machines as well. Here are a few general rules that I use when applying GD&T.
-The purpose of GD&T is to REDUCE overall tolerances and manufacturing costs. If your part is getting more complicated and/or expensive, then you are either not applying it correctly, or you don't need the GD&T. For every Geometric Tolerance added, there should be a few other tolerances opened up.
-Concentrate only on the key function of the part and it's critical features and hold these only as tight as necessary.
-There is usually more than one way to specify a functional characteristics of a given part. Select the one that best suits the actual machining or manufacturing operations performed on the part. If in doubt, use the simplest method.
-Always keep in mind how these tolerances will be measured and verified. Production gauging can become very expensive, and one-off parts can be tricky to check if you don't have a CMM in house.
-For most turning (Lathe) operations, I use Circular and Total Runout to instead of more complicated tolerances like Perpendicularity, Cylindricity, etc... The parts can be more easily measured, and the results are the same.
-Keep in mind that positional tolerances are based on radial tolerance zones, not X-Y deviation. This means that you can open-up tolerances and maintain functionality. Production & NC machining can work well with this, however, I wouldn't recommend using them in a standard machine shop.
I hope that these pearls of wisdom are of some use to you. Some people may disagree, but these rules work well for me.