Our team has designed co-processors for smart sensors in the past, and most of our boards come through
expressPCB . They have a proprietary board design software application that is pretty good, and decent libraries - the only downside I've found is no autorouting, but most free autorouting applications I've used are horrible. One of the great things about expressPCB is the miniboard option - you can get three 2-layer 3.8" x 2.5" PCBs for around $50, sans silk screen and with a limited number of vias and holes. Most of our boards were considerably smaller than that, so we often shoehorned 2 or 3 separate circuits onto the surface provided. Great stuff.
Their schematic linking program is nothing special, but works well with the layout program. Pretty much, having used PCB123 and PCBexpress, I can safely say that I prefer expressPCB.