Although they used some innovative techniques to get the arial shots (including remote controlled gliders and helicopters to get the cameras in formation with the birds), the film has also gotten some criticism for distorting reality. See:
http://www.bayarea.com/mld/cctimes/5936787.htmBut I don't think it detracts from the fact that there is some spectacular aerial footage in this film.
The official web site of the movie has some info on the aircraft used, click on the "The Production" (second link from the top, site requires Flash):
http://www.sonyclassics.com/wingedmigration/home.html-Matt