I've been using the Dvorak keyboard layout for a few years, and something that's always bothered me is keyboard shortcuts. On a QWERTY keyboard copy and paste are conveniently positioned as Ctrl+C and Ctrl+V, but on Dvorak they are pretty inconvenient (equivalent to Ctrl+I and Ctrl+. on QWERTY).
I would have figured the 'right' thing to do would be to have the keyboard shortcuts based on position, rather than value. So switching to Dvorak would change copy and paste to Ctrl+J and Ctrl+K (which are in the same position as C and V on QWERTY), but very few applications do this. In fact, the only one that comes to mind is Inkscape. I get that implementing it that way is harder, but not even Windows does it, so I figure there must be some further reasoning behind it?
I'm also interested in how certain international keyboards are handled, such as Arabic and Russian keyboards, which don't have any Latin characters.