To clear *all* messages from the queue, shut down qmail, then:
cd /var/qmail/queue
find intd todo local remote mess info bounce -type f -print |xargs rm
Start qmail back up, and the queue should be empty.
To just clear the "stuck" messages, you'll have to define what you
mean by "stuck".
Source: http://msgs.securepoint.com/cgi-bin/get/qmail0308/128/1.html