I'd recomend 1/2" in acrylic. Remember that you'll need some substance to span the gap, between the inlet and the baseplate. I'd only consider 1/4" in polycarbonate (but I'm still going with 1/2"
). I'm opting to glue two sheets of 1/4" together, to make that 1/2" thickness. IPS Weld-On #4 will do this with a clear finish, for polycarb or acrylic.
1/4" thick copper would be perfect for a start. Many DIY block-makers here use RTV silicone to seal their blocks. Goop is mostly clear, but if you seal it around the edges, it'll look just fine, regardless of the color.
I can't really advise you on how deep the center hole should be, that's really up to your design. One factor to consider is how large it is, compared to where it sits over a CPU core. Other than that I can tell you that the fins on White Water and Radius are less than 5 mm high, actually 4mm high if I remember right.