History shows a few approaches of handling isometric controls.
The oldest game to use absolute isometric controls I can think of is Q Bert:
This was usually played on the joystick - which had 8 directions, not just the 4 arrow keys. Interestingly, though, instead of using diagonal movement on the joystick. you were supposed to tilt the whole joystick, enabling a far more comfortable control experience. Up, left, etc. mapped well to the screen this way.
Of course, doing this with the keyboard is rather clunky - even more so when you realize that the arrow keys actually aren't symmetric - the down key is usually between left and right, making this even more clunky. However, the numeric keyboard is commonly used for navigation as well. In fact, when you turn your numeric keyboard off, provided you have a desktop keyboard, 4 is left etc. This allows you to control isometric movement quite easily using 7, 9, 1 and 3.
And again, the numeric keys for that also map to other keys on the keyboard - Home, Page up, End and Page down. On traditionally layouted keyboards, those can also be used, even when not using the numeric keyboard - they form a nice square that maps perfectly into isometric controls. If you only allow isometric movement, this is incredibly easy to use - if you also want to allow movement accross (i.e. straight up/down etc.), I'd suggest using the numeric keyboard instead - but of course, if you go by virtual keys, there's no difference between Home on the numeric keyboard and the other Home key. If numlock is off, of course :)
Of course, the old trick with a joystick can just as easily be handled with gamepads on modern computers - although it usually isn't necessary (or worth the worse ergonomics), since modern gamepads are usually quite easy to with diagonals.
The last option would be the mouse - this is most useful in games where the world is isometric, but not a fixed movement grid - you're moving in any direction you want, and it's just the rendering (and terrain etc.) that's actually grid-like.
Notebook keyboard are usually the trickiest. Even if you do have some nice cluster of keys that could be used comfortably, they usually aren't aligned in a perfect square, which hurts a bit. In the end, make the controls configurable - different keyboards have different ergonomics.