Well, I've been reporting the answer of Altera support in this regard in a previous thread. I'll add the link later on. My question was about a documentation of Virtual JTAG codes, particularly the device and instance selection. Support suggested to use the tcl shell to learn the codes... In the meantime, the situation has get better, because the new Virtual JTAG user guide contains some useful information.http://www.alteraforum.com/forum/showthread.php?t=1686
The connection of SignalTap and Virtual JTAG exists, if you intend to access the virtual JTAG instance directly without the stp application. Personally, I don't plan it yet, but it can be interesting, too.
Virtual JTAG is a suitable interface to operate e.g. a test and calibration tool just through the standard JTAG header that is provided anyway for configuration memory programming. It would prefer this as a product feature rather than hacker knowledge.