Is it possible to open a pop up from a Java page which is on Safari browser to open a popup in IE browser. I think it is not possible.
Good question! ;-) I too think this is not possible as the file will be opened with the default program associated to it.
Edit: Some investigations did not give me much information. Is it not possible with javascript too. More over if the user is using IE or FF then it was his decision. Why should you open another application without his permission. And I don think Browsers will allow this due to security issue even if this is possible.
You shouldn't assume that the user has IE available.
Some applications can be launched from the browser (if the user has them installed). For example, itunes://, ftp://, etc.
To answer your original question, no, you cannot. It would be a security risk if you could arbitrarily launch applications on the users machine.