Can I make applications load on the same monitor as the mouse cursor?
I think Mr. Siracusa has railed against the lack of consistency or flexibility that leads to a situation like this, and I don't have a "you can modify this plist and presto!" answer either, but I saw this and thought of your plight:
cordlessdog.com/stay/

It may not be what you need, but it could be a step in the right direction, which I heard of here: http://twitter.com/wilsonminer/status/20750686482