I chose to use the bridge type. That is, both Y-axis rails are horizontal. And the z-axis is mounted inbetween.
This way the weight is more evenly distributed as well as other forces. See Finagling the Gantry in a previous post.
Actually, I don't think it matters that much if you have a stiff design. But seeing as how this is my first router and it's pretty big I decided to give myself the best chance of it working ;-)