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I have no idea if Windows Server 2008 runs Java applications better than 2003 but, regardless of which you run, here are a couple of ideas that may be of help:
1. x32 Java/SQL Developer starts up with a smaller working set (246,000 KB) than x64 Java/SQL Developer (318,000 KB).
2. Try tweaking the garbage collection algorithm, using Garbage-First:
Re: Memory Leak or Bad Java Garbage Collector
I ran across this (old) comment from a blog on blogs.msdn.com:
Even though Windows Server 2008 R2 is exclusively a 64-bit operating system, 32-bit applications are supported by enabling the WoW64 optional feature. If this feature is not enabled and you try to run a 32-bit application, the application will fail to execute. The WoW64 execution layer is an optional component that is installed by default on R2 releases after beta1. You can save resources by removing the feature if you are not going to be running 32-bit applications on your Server Core install.
SQL Developer Team
Thank you for your input. I will have a look. In any case, I will leave the question open for a little bit more, should anyone have better suggestions.