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In my current setup (debian squeeze x64, 6 cpus) neither java nor apache seem to utilitze the full potential of the server. The munin monitoring shows cpu usage never exceeds the 200% mark. We ran several stress tests which raised the server load up to 80, but the cpu usage always remained low. Any ideas?

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Have you double-checked that the CPU usage really is that low? It's entirely possible that Munin graphing does not work as expected and if observing the server from shell with top or other utilities, CPU usage is working as expected. –  Janne Pikkarainen Jun 9 '11 at 7:03
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Have a look at this document about optimizations for running on multi-core systems

There's a heap of stuff in there, everything from how to structure code to stuff like numactl for controlling processor affinity.

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