To clear *all* messages from the queue, shut down qmail, then:
service qmail stop
cd /var/qmail/queue
find intd todo local remote mess info bounce -type f -print |xargs rm
service qmail start
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