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I was wondering if there would be any implications (slowed performance, crashes and so on),
running a java 1.4 application and a java 1.6 application on the same machine
Different
javaversion are installed in different directories so running 2 java programs with different JRE version will not make any effect other than that you are running 2 processes of java.So bottom line, there is no problem with that, it will not slow you down.
Also, java 6 has better performance than 1.4 so if you can run both on 6 its usually better.