First get the process id using
ps | grep java
then send the quit signal
kill -QUIT <your-pid>
But this was not working for me on my server running Jetty 6.1 as installed by the .deb installation. The logs showed nothing.
After a bit of searching on the interweb I found the new (to me) method of generating stack traces using
sudo jstack <pid>
This was slightly more helpful and told me:
"Unable to open socket file: target process not responding or HotSpot VM not loaded"
At last I had something to go on and found that jstack must be run as the same user as the java process - which in the case of Jetty as installed by the debian install files is "jetty"
sudo -u jetty jstack <your-pid>
worked a treat and so did
sudo -u jetty kill -QUIT <your-pid>