What case is "this case"? How long does your VM take to start? What & how  
many libraries / packages are you linking to?

A couple notes:

* make sure when you start the VM, be sure to pass "-client" on the  
command line. This will, among other things, favor startup time over  
runtime performance.

* Use a JRE from www.java.com, not a JDK. The JREs are built with almost  
no debugging included, making them just a smidgeon smaller and faster than  
a full JDK (though the -client VM may be the only option when using a JRE).

* Try using Java 6 and Java 5 (if your app is compatible). For most users,  
Java 6 is a tiny bit faster at startup, and can cut out a second or so.  
For other apps, Java 6 can be A LOT slower. I can think of a couple apps  
that open with a Java 5 VM in less than 10 seconds, but require well over  
a minute using a Java 6 runtime. So, for some special cases, it may be  
better to stick with Java 5.

* Most use cases consider 5 second VM startups to be acceptable, in favor  
of optimizations in the runtime performance, rather than trying to  
minimize startup time. There are plenty of optimization options, but you  
should consider looking at a non Sun VM, or a solution that does not  
require a VM (eg: using a native java compiler).

What kind of JNI are you doing? If you are loading native libraries at  
startup, check and see how many libraries your native functions are  
linking to.

Have you tried calling your native functions from a C app just to compare  
how long your native code takes to load?

Sounds like you may need to run a profiler on your app to look for  
hotspots in the startup time...

HTH,

-Zig