Here's one I didn't anticipate:
I kept the 27" Araya rims laced to Suzue cartridge bearing hubs from my Shogun touring frame to use on the Schwinn Voyageur frame that I received in trade for my Shogun frame (see the frame pass-around thread). The Schwinn has vertical rear dropouts, while the Shogun as horizontal dropouts. Both bikes have 126mm rear spacing. However, the rear wheel won't fit in the Schwinn dropouts because the drive side dropout has a 9mm wide opening and the axle is 10mm thick! The non-drive side dropout opening is 10mm wide and the axle fits fine.
Here's the dilemma: the Q/R axle can't be swapped for another, because it's designed for sealed cartridge bearings. The axle flanges against which the the cartridges seat are spaced exactly for this hub.
The only alternative I can think of is to file down the threads on the axle to create flats. 0.5mm on each side would do the trick. Is there any downside to doing this?