The key is to have the Tridion java wrapper fire up the JVM in debug mode:
java -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=1044 -Djava.compiler=NONE -Xnoagent
The rest is business-as-usual remote debugging with Java.
Tridion appears to set
jvmLoader.Debug = true; by default. So you should just be able to attach to the java process that Juggernet starts as you would normally without doing anything special for Tridion.
Otherwise, Tridion Content Delivery tries to read a file called jvm.xml in the tridionhome or bin folder (unfortunately it will take a bit more hacking to figure out the format of this file). If Tridion doesn't find this file it looks in the Registry:
@Software\Wow6432Node\Tridion\Content Delivery\General for keys that start with jvmarg1, jvmarg2, and so on.
If the keys aren't present it defaults to what I mentioned above.
So you should be able to create a new set of keys and then simply attach to the java process the normal way you would when doing java remote debugging:
Keep an eye on the log when you start up the app pool as there will be messages logged regarding what keys got loaded or errors if it can't recognize the keys.