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Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run]
"ApacheTomcatMonitora"="\"C:\\opt\\tomcat\\bin\\tomcat6w.exe\" //MS//Tomcat instanceInstance tomcat-a"

Save the file as Tomcat6a-system-try.reg

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tomcat6w.exe "//MS//Tomcat instanceInstance tomcat-a"

Finally log out and log back in. You should now see the tomcat icon on the system tray.

Setup Tomcat B

To set up another instance of Tomcat, I would call it tomcat-b, simply copy the tomcat-a directory, change the ports as outlined in Ubuntu 5.0 Portable Tomcat 6.x & Instances and repeat Automatic Startup and Shutdown of Tomcat and Tomcat Icon on System Try with adjustment for the different name and directory.

References

http://tomcat.apache.org/tomcat-6.0-doc/windows-service-howto.html#Tomcat6w - Background on how to add to system try.