Your lack of specifics indicates more research needed. I suggest starting at builditsolar.com. Glazing choice depends on the type of collector. I can tell you that double glazed polycarbonate (greenhouse type) will not hold up for flat panel type hot water or air collectors; the temperature gradient between inner layer and outer will make the panels bow and warp, prematurely failing. I switched to single layer 1/16 polycarbonate which works fine, but doesn't perform as well in very cold weather, and you should design your collector to accommodate the expansion and contraction from heating/cooling.
If money is no object than double glazed tempered glass (high transmission) would be hard to beat for flat panel collectors.
