1. A three-dimensional annotation method comprising: obtaining a source image that is two-dimensional or three-dimensional; displaying said source image on a screen associated with a first computer; accepting an annotation associated with a desired depth of a region within said source image via an input device coupled with said first computer; obtaining at least one depth associated with said annotation; wherein said at least one depth corresponds with said desired depth of said region; and, annotating said source image with said annotation at said at least one depth in a three-dimensional image; generating an annotated stereoscopic image that comprises left and right eye views that differ from each other having said annotation at said at least one depth that differs from a depth of said region; and, generating an output stereoscopic image with said region at said same depth as said at least one depth of said annotation.