There was also a good presentation at JavaOne in 2003 (I think) entitled "The Black Art of Benchmarking" about things to avoid when writing a benchmark. You might want to check if it's publicly available.
BTW, the key to writing a good benchmark is to make sure and profile your benchmark to ensure you're actually testing what you want to test.
Another source of benchmarks is the spec organization. www.spec.org. They publish some of the most well known benchmarks in the industry. The current jvm benchmark is quite old and in the process of being update, but it's still worth checking out if you're trying to do a survey of java benchmarks.
Here are some links.
An extensive list of papers on virtual machine performance - almost all of them have benchmarks.
An online comparison of JVM's with some standard benchmarks.
The guy - Shudo - appears to read this list
The DaCapo benchmarks - recently released under the Apache SoftwareLicense. (yay!)
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