Actually, I've been using the JK2 ISAPI  connector with IIS 6.0 (in
worker process mode) just fine. If I'm not mistaken, I've also had the
JK ISAPI connector running under IIS 6.0. I think the key is loading the
filter at the site level and not at the global level, and making sure
the site has its own application pool. I can investigate this further as
I may be moving to JK eventually anyway.
 
In IIS 6.0 "worker process mode", you have one or more application
pools in which all ISAPI filters and applications are executed. No
third-party code ever runs in-process with inetinfo.exe. Each
application pool consists of one or more worker process that handle
requests. Additionally, the worker process are recycled after specified
intervals to reclaim resources for any leaky applications you have, plus
there are some health checks that help prevent situations that would
have caused IIS 5 applications to hang or become unresponsive.
 
In IIS 5.0 isolation mode, you're back to low, medium, and high
isolation levels. ISAPI filters run in-process with inetinfo (gag) in
IIS 5 mode. In low isolation, ISAPI applications also run in-process
with inetinfo.exe, but thin medium or high isolation they run in
dllhost.exe.
 
I wouldn't use IIS 5.0 isolation mode unless I had no other choice. I
can't over-state this.

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