What is the best way to use two 27" monitors on your desk?
You don't say what you'll be using them for.  I'm (among other things) a programmer, and for me being able to see a tall vertical area in my text editor is of primary importance.  Thus, given 2 widescreen monitors, I'd set them up vertically, next to each other.

I'm not unique here: when I visited Google, most of the programmers I saw had this layout too.

I would think this could help with your neck problem, since it makes the display area closer to a square, and not a really wide rectangle.  Alternatively, you could keep them horizontal, and stack one right above the other.  Depends on the shape of the things you're going to be looking at most, I guess!