There are "big" (and usually expensive) boundary-scan tools which can 1) generate test vectors from PCB netlists and 2) allow to develop, debug and run high-level scripts to do boundary-scan testing, clusters (non-JTAG devices) testing and flash programming.
Have a look at:
http://www.xjtag.com (
http://www.xjtag.com)
http://www.jtag.com (
http://www.jtag.com)
http://www.flynn.com (
http://www.flynn.com)
www.asset-intertech.com (
http://www.asset-intertech.com)
www.goepel.com (
http://www.goepel.com)
http://www.corelis.com (
http://www.corelis.com)
And there are "small" affordable boundary-scan tools for prototyping and developing which allows to monitor and control pins states.
Have a look at:
http://www.topjtag.com (
http://www.topjtag.com)