I have constructed a number of synthesizer modules, based on the Doepfer module size and power format.
I design and layout the printed circuit boards using the free Eagle CAD program, and get the boards fabricated by AP Circuits. The freeware version of the Eagle program has a size limitation of 3.2"x4.0" (100x80 mm), but I have found that this size is more than enough for Doepfer size modules. The APCircuits boards are rather expensive in small quantities, but no more so than other PCB companies. They have a very fast turnaround, and being in Canada there is no holdup at customs (for Canadian customers!). The cost of boards and shipping is typically around $100 CDN for two. Most of this cost is the setup cost, which is the same no matter how many boards you make.
I have the front panels made by Frontpanel Express, a spin-off of the German firm Schaeffer. They do a very nice job, and price is around $30-40 per panel for a standard Doepfer size. Delivery time is a couple of weeks. You can get express delivery, but this doubles the price.
A lot of the parts for the modules I have had lying around at home from previous projects. Most of the new parts I get from Digikey, since they have an extensive selection and are reasonably priced. They also have a Canadian web page and distribution which is very convenient and makes for quick shipping. Usually I get the parts 2 days after ordering.