My desktop native resolution is 1920 x 1080 however Witcher 2 configuration only allows me to pick from the following resolutions:
640x480
720x480
720x576
800x600
1024x768

I've tried setting my resolution higher in the ini but that just returns a DX9 error and resets it back. Are these the only resolutions I should be selecting from or is there a way of selecting something higher than 1024x768 (I want a 16:9 one)

My only suggestion is to try running in a fullscreen window, if that is an option.

I had a similar problem with Bioshock Infinite where it would only let me select 800x600 and 1280x720.

The only solution I ever found was to run in fullscreen windowed mode.