I'm a little confused that you're asking this, so please clarify if I'm misunderstanding.

Right now I have 5x WoW open on one computer. One window is active (or would be if I wasn't tabbed into FF) while the other four are visible but do not have focus / are not "selected". They receive keys just fine (as parsed by my DNP list) - which is what Keyclone DOES. Without Keyclone (or an alternative solution), only the window with focus would react to keypresses.

I don't know anything about boxing EQ2 other than that it can be done. I don't think Sony has any official objections seeing as I see EQ2 threads all the time, and EQ has been boxed since time immemorial - but I don't know, since I don't play EQ1/2. Check the wiki.