coincidentally I checked the runout of a spare axle I had on hand. I have no idea if the runout (about 0.013� in the middle) is anything to worry about, but I posted the method and a video on my blog.

http://shufti.wordpress.com/2014/02/09/vanagon-measuring-axle-runout/

One can imagine that even slightly bent axles would have an effect on driving smoothness and perhaps have an effect on bearings and cv joints

alistair