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By "application", I'm assuming you mean different web/ejb/enterprise applications within a single SJSAS instance. If that's true, then the answer to your question is no -- all applications share the resources of the appserver.
On the other hand, if you need to, you can set up multiple instances of the appserver on the same machine, deploy one application to each instance, and control the resources that the appserver itself uses. How you limit the CPU use (and monitor) is then done at the OS level -- I don't know how it's done in Linux, actually. But in Solaris, you could use the Solaris Resource Monitor, or processor sets, or Zones/LDOMs, or any number of things to affect the resources available to the appserver; look for similar things in Linux.