A servlet solution might work for this. If you use the <a></a> with
the target property, you could have the link hit the servlet and
redirect content into the new target window. Possibly, in order to
keep track  of the window, you could assign an arbitrary ID or name to
each child window  that is propagated through submits and anchors. Then
when the servlet processes the request, it will know what to do and
who is asking for it.

Do you need more control than this?

Yes it is possible.
If it is at the same level fine, Use a array to store
the reference of all. (But the parent window  shld not
be refreshed / change the page)
But if it is multi level, then it is tough.
You need to maintain at each level for the child
windows and if required passed to the respective
parent window.

Here also we have the same condition, no page refresh
/ change on the parent window.

Where and how are you getting the reference from? What kind of
architecture are you prposing? Is this a servlet model or a standalone
on a desktop model?

Another option I thought of involves a bridge between an Applet and
Javascript. Not sure if this bridge is still available, but I used it
about 2 years ago. If this is the case, Javascript can do all the work
and report to an Applet that will talk to your application.