Transcriber is being completely redevelopped by Bertin Technologies and should be released by Q2 09.
That new version will be based on Annotation Graph, which will be the default format of the new annotation files. In a nutshell, an Annotation Graph represents linguistic annotations of time series data as a formal graph. An AG also abstracts away from file formats and provides a logical layer for annotation systems.
A beta version should be available in a couple of month.