I need to set up GeoNetwork on the same server as GeoServer (Windows server 2003, with IIS6) .
Is it best to use multiple instances of Tomcat or put both web archives in the same one? They both need to listen on the same port 8080.
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You cannot have different tomcats listening to the same port.
Said that, it is good to have separated tomcats for big java apps, just because if one of them have problems like running out of memory, you can restart that app without having to bother the other app. Running out of memory is common for certain use cases on geoServer. So, it really depends on your use case.
My suggestion: have an apache listening on port 8080 and two different tomcats (for example on port 8081 and 8082) with geoNetwork and geoServer. The apache can redirect to this other tomcats based on UrlRewrite or domain name.
I think so, but I would check this guide for more information: http://geoserver.geo-solutions.it/edu/en/clustering/load_balancing/microsoft_IIS.html
Personal note, expose them on port 80 rather than 8080. Many close environmente won't let people access a link with port different from 80.