xc3sprog is command-line tools for programming FPGAs, microcontrollers
and PROMs via JTAG.
Homepage: http://xc3sprog.sourceforge.net/
I'm using the latest from subversion as xc3sprog doesn't seem to make
proper releases. There are only a few seemingly random snapshots at
sourceforge. And these snapshots are built binary packages, not source
archives.
NOTE: I haven't tested this on any hardware yet.