Being a Mac OS X user, I've implemented a popup engine which slides from top (transition is about 300 ms, see video) and stays hooked to the top.
Most people (all developers at the moment) say they're not used to it. They feel better which the classic approach, where the popup is centered.
Eclipse's behavior is different on both OS, but I can't afford both. Put aside the design aspects, which is the best cross-platform behavior in terms of user experience?
Note: I know these screenshots are full of UX errors (Eclipse…), I'm only concerned about the position and transition of the popup.