Open-source FPGA http://www.eecs.berkeley.edu/Pubs/TechRpts/2014/EECS-2014-43...
Open-source, bitstream generation for Xilinx http://drop.isi.edu/sites/default/files/users/nsteiner/soni-...
Open-source tooling for lattice http://www.clifford.at/icestorm/
Open-source EDA flow http://opencircuitdesign.com/qflow/
Older, academic tooling for FPGA's http://www.eecg.toronto.edu/~jayar/pubs/rose/rosefpga12.pdf