Spencer Webb runs AntennaSys, a company that designs tailormade RF solutions, and has himself worked on making quad-band transceivers for AT&T. As he tells it, almost all phone makers have now transitioned to locating their antennae at the bottom of the phones. This has been in order to move radio wave emissions away from the head (a shortcoming that a top-mounted aerial would incur), which the FCC has been quite demanding about with its SAR standards --
The iPhone 4, however, moved the antenna action from the back of the phone to the sides. This probably improves the isotropy of the radiation pattern, but only when the phone is suspended magically in air.
Another great point made here is that testing done both by the Federales and mobile carriers might include the head, but never accounts for the presence of the person's hand. Thus, although a phone's antenna could test very well, it might suffer from such issues as those experienced with the iPhone 4.