At least it think that is not question of java version 1.3 or 1.4 more a question of the servlet specification and the implementation itself.
For example I person have the experience that jetty is much much faster then tomcat.
Do you have more improvement suggestions?
If you want Java web container performance, have you tried out Resin? I'm not performance expert, but Resin gets really high marks. jGuru (which uses Lucene) is driven straight from Resin with not even Apache in front.
Erik
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