EECG, University of Toronto
http://www.eecg.toronto.edu/~jayar/software/software.html

FPAA opencircuits
http://opencircuitdesign.com/~tim/research/fpaa/fpaa.html

JHDL
http://jhdl.org/

libhdlfltp
http://sourceforge.net/projects/libhdlfltp/

OpenCiphers
http://openciphers.sourceforge.net/oc/

OpenCircuits
http://www.opencircuits.com/Main_Page

OpenFPGA
http://www.openfpga.org/pages/Resources.aspx

Static Free Software
http://www.staticfreesoft.com/productsFree.html

TCAD software
http://www.tcad.com/tcadcentral/Software.html

USB FPGA project
http://www.fpgaz.com/usbp/

Wireless Open-Access Research Platform (WARP)
http://warp.rice.edu

Yet Another Small Embedded Processor (YASEP)
http://yasep.org