I have a Tomcat running as a Windows Service, and those are known not to work well with jstack. jconsole is working well, on the other hand, and I can see stacks of individual threads (I'm connecting to "localhost:port" to access it).
How can I use jconsole or a similar tool to dump all the thread stacks into a file? (similar to jstack)
You can use the ThreadMXBean management interface.
This FullThreadDump class demonstrates the capability to get a full thread dump and also detect deadlock remotely using JMX.