[cnvogel]

The program counter will not typically be compared via JTAG (this would be way too slow) but there will be dedicated registers inside the CPU that are compared against the program counter.

For AVR specifically, have a look at e.g. https://github.com/raimue/avarice/blob/master/src/jtagbp.cc (just random find on github, likely not the official repository).

This is, by the way, also possible on a typical PC (as in "personal computer" not program counter), also x86/64 has debug registers.

http://www.codeproject.com/Articles/28071/Toggle-hardware-da...

...and very likely also on ARM, m68k, MIPS, Sparc, PPC, ... I just didn't look it up.