I have a java desktop application for searching files and it is usually reaching the default heap limit pretty soon. I wont have access to all the systems it will be install
There is no such standard API to do so.
I would suggest you use Java Web Start to invoke your application (can be used for local applications to in the latest Sun Java 6) as it allows you to specify values for this.
You can then have three or four links each pointing to exactly the same files but with "Tiny", "Medium", "Large", "Gigantic" heap sizes.