JTAG boundary-scan test software to view and control pin states

Take a look at TopJTAG Probe -- http://www.topjtag.com. It seems intended to what you've described. A good news it works with several popular JTAG pods so you probably don't need to buy additional JTAG pod but use yours existing.

Another option might be the free Buzz utility offered at Jtag Live That also works with Xilinx and Alter cables and possibly FTDI chip based cables.

It allows you to 'watch'a signal using SAMPLE mode and buzz out mutiple connection between JTAG devices - pretty neat really.