If we produce our own FPGA board then the cost comes nearly Rs.5000, currently am preparing schematics to design a low cost FPGA board. it will be ready within two months. The prevailing FPGA boards are costly due to their peripheral features. If we do any research based FPGA, sometimes the peripheral may not help us or simply its enough to have FPGA board with input/output expansion connector. We can analyze the results with the help of DSOs or Spectrum analyzers.
I mean the external peripherals such as switches, LEDs, and relay interfaces, etc.. We have to maintain the minimum hardware requirements such as crystal oscillator, all kinds of power supplies. If we have the FPGA routed to the IO connectors then we can do the specific application interfaces.
In-house developed FPGA boards can be very costly too. With current FPGAs and current speeds, you need at least high-density four-layer PCB design and manufacturing, able to solder ball-grid chips. Nether PCB software nor manufacturing is cheap. The same holds for expansion connectors - they are either expensive or they are a signal-integrity nightmare. All depends on your existing abilities and cost structures around.
Few years back I also encountered the same problem while working with Xilinx Spartan-3 FPGA.
When you think that we should have our own board, then the overhead/setup charges are more than the actual PCB cost and ultimately you land up in a higher cost even if for initial 5 boards trial run. Therefore multilayer board is not an economical solution particularly for the academic setup.
But that does not mean you have to invest in the costly boards.
Work out your I/O requirements. For academic use, it will certainly less than 100 count/pins. There may be some exceptions to this although! Then select the TQFP package of your FPGA chip. In the market, you can get adapter PCBs for up to 100pin TQFP. The connection are brought on all the four sides with a 0.1" or 0.05" pin spacing connectors. Thus, you can then just develop a low-cost 2-layer motherboard where this FPGA board can sit as a piggy-back card.
As far as the connections are considered, important are the CLOCK, JTAG and POWER. And you can only use the required I/O pins for the connections on the double sided motherboard.
And on the mother board, you can always have your peripherals to suit your exact needs.
Check out for some suppliers on Lamington Road, Mumbai for a ready-to-use board but you may get such adapter boards fabricated from your local PCB suppliers. It is not necessary to use a BGA package so TQFPs are the best to start with.
I think your question is too common to be answered... What is your design - the FPGA can be seen as a highly configurable computer, if I can call it like that, so you can solve really lot of very high speed parallel tasks with it.
First of all you should refine your goals - what are the I/O requirements, capacity in terms of logic (each manufacturer has slightly different terminology for that), speed and so on. I doubt you can beat the price of a development board by building a prototype by yourself. The main difficulties will be the signal integrity issues (someone call them a "black magic" - it can be a real nightmare if you have limited experience) and the multilayer PCBs because of the unfriendly BGA footprints; in many cases you can have power supply issues as well. This can force you to iterate several prototypes before getting a reliable one and that will raise the price to the sky.
In general I have used boards from Digilent Inc. that are very good for the lab and they have "academic price" option for many FPGA boards. Also you can check Trenz Electronic (http://www.trenz-electronic.de/) who offer simple and also not so simple SoC modules with FPGAs - they can be used as a well tested FPGA core modules for a mainboard that you can build much easily and populate with the necessary peripherals. If you are looking for a simpler design you can check Numato Lab (http://numato.com/fpga-cpld) in Bangalore, India or the Papilio (http://papilio.cc/) project which is open source.
No matter of what you are doing my opinion is that it is not cost effective to build an FPGA board yourself unless you have some very specific needs.
I agree with you but for our project we need custom FPGA Board. So we are trying to make it. We are having good PCB fabrication facility in our department.