Profiling of the applications launched via webstart may sound difficult, but in reality it isn’t. What you need is to have approriate profiler/debugger native libraries in LD_LIBRARY_PATH of the system (or equivalent), and then specifying necessary arguments for webstart (from command line)
For example, using YourKit with Webstart:
[code]
javaws -J-agentlib:yjpagent=tracing http://example.com/example.jnlp
[/code]
Same approach works as easily for remote debugging/profiling in Eclipse, JProfiler, etc.
Update: 5.6.2011
Sadly Sun broke this around JDK 1.6.0_10, and since that neither debugging or profiling of Webstart has worked properly. Especially debugging of webstarted application it not working at all. Shame on you Sun (well, Oracle nowadays).