How to design a Spartan-6 PCB?
The Spartan-6 LX9 is available in the hand-soldering-friendly TQG144 package ([UG385] v2.3 at p. 30). Numato designed an open-hardware board around this FPGA/packaging: the Mimas Spartan-6 devel. board [NUM1]. The KiCAD [1] schematics and PCB layout files are found in Numato's SVN repository at [NUM2]. In addition, Numato created a component description file for this packaging: XC6SLX9-2TQG144C.

Numato's Mimas PCB
Other examples of a Spartan-6 PCB design
Andrew Zonenberg has a pretty interesting blog [2], where he used a Spartan-6 mini board. The schematics are available there: [3].
Chris McClelland also made his own Spartan-6 development board as open-hardware there: [4].
Kevin Modzelewski discussed the design of FPGA board here [5], and made a simple breakout board for the Spartan-6: [6].
The Scarab Hardware team designed an open hardware Spartan-6 LX9 board and had a Kickstarter campaign to fund it [7]. Eagle source files can be found there [8].
Jack Gassett designed the PapilioPro board featuring a Spartan-6 LX9 in TQFP-144 package [9]. Schematics can be found there [10] (the schematic routing is quite neat).
How to design a STM32-F4 PCB?
The STM32-F4 was chosen for bit-banging the configuration of the Spartan-6 FPGA. In its smallest packaging (LQFP64), a very compact board can achieved. Frank Zhao designed a bread-board-friendly breakout board for the STM32F405RG [11]. The EAGLE [12] design files can be found at [13].

Frank Zhao's STM32F4Stamp PCB
References
[UG385] | Xilinx Spartan-6 FPGA Packaging and Pinouts http://www.xilinx.com/support/documentation/user_guides/ug385.pdf |
[NUM1] | http://numato.com/mimas-spartan-6-fpga-development-board.html |
[NUM2] | Numato SVN repository instructions http://numato.cc/content/how-checkout-files-numatocc-svn-repository |
[1] | Silicon exposed blog, http://siliconexposed.blogspot.de |
[2] | http://azonenberg-devboards.googlecode.com/svn/trunk/boards/minimal-spartan6-tq144/ |
[3] | https://github.com/makestuff/lx9 |
[4] | Kevin Modzelewski's blog, http://blog.kevmod.com/2013/09/choosing-fpga-parts/ |
[5] | Kevin Modzelewski, Spartan-6 Breakout v0.1, https://oshpark.com/shared_projects/duLs3P1R |
[6] | miniSpartan6+, kickstarter campaign, https://www.kickstarter.com/projects/1812459948/minispartan6-a-powerful-fpga-board-and-easy-to-use |
[7] | miniSpartan6+, Eagle schematics and PCB files, https://github.com/scarabhardware/miniSpartan6-plus |
[8] | Gadget Factory, PapilioPro, http://papilio.cc/index.php?n=Papilio.PapilioPro |
[9] | PapilioPro, https://github.com/GadgetFactory/Papilio-Pro/blob/master/BPC3010_Papilio_Pro.pdf?raw=true |
[10] | KiCAD official website http://www.kicad-pcb.org |
[11] | STMicroelectronics STM32F405RG Product page http://www.st.com/web/catalog/mmc/FM141/SC1169/SS1577/LN1035/PF252144 |
[12] | CadSoft EAGLE http://www.cadsoftusa.com/eagle-pcb-design-software/about-eagle/ |
[13] | Frank Zhao's STM32F4Stamp http://eleccelerator.com/stm32f4stamp-breakout-board/ |