To be honest, I didn't try it myself. I just checked that it started using wine.
There are three problems with it:
1. It doesn't find the jackd.exe binary. I don't know how the path is handled
in qjackctl under windows. Maybe the problem is that it was a 32 bit build
of qjackctl and a 64 bit build of jack?
2. Scanning for the available pulseaudio drivers takes many seconds.
qjackctl freezes while this happens.
3. When choosing the direct sound primary sound driver (in many
cases the most natural driver to try), jackd says (on one of my computers) that
it can't start the driver because of illegal input and output arguments (I think).
This information is written to the console. However, qjackctl just says in the
messages window that it crashed, and doesn't show the information printed
to the console. Perhaps it's not possible to redirect this information to the
messages window?