Heh. As a dvorak user I'm often annoyed by this as well. It's usually not an issue as you can switch the layout with a keystroke, but sometimes games seem to continue using the incorrect layout and you need to restart the game with the layout set beforehand.
This. Computers can be really bad sometimes about handling different default keyboard layouts. I've had some games that end up binding the same letter to multiple keys, which renders other letters inaccessible! Bizarre. And while you can switch back to QWERTY easily enough, it's still jarring switching back and forth.
Using arrow and modifier keys is nice because they never get remapped, but being right handed, I'd rather have the action keys and not the movement keys on the hand with better reflexes.
Odd, I prefer to have movement on the right hand for the same reason.
And yes, using arrow keys and meta keys is good, not just because they don't get remapped, but also because you're much less likely to run into the "key limit" with meta keys, since they're designed with the assumption that many of them may be held down at the same time.