From what I know of 3D printing, it's going to be huge. The potential seems to be that if you can design something (using 3D design software) you will be able to send the file to a printing company, and they will produce the part(s) in whatever quantity you need. Obviously you are limited to plastic materials, but I think there wil be a fairly wide range of finishes available. Prices will plummet as the technology becomes cheaper and more widely used. 3D printing is already being used widely in the custom automotive industry (replacing unavailable knobs, dashboard parts etc), and there's no reason why it shouldn't be used in musical applications. Synth manufacturer Teenage Engineering has already adopted the technology:
http://boingboing.net/2012/10/01/popular-synthesizer-manufactur.html
I'm hoping to re-knob my Pollard Quad syndrum!
Unfortunately if you want custom metal parts, you'll still have to resort to conventional milling techniques which will remain relatively expensive.