Data format used within Transcriber
A transcription file created by Transcriber is in XML format and its syntax is described by its DTD. You can look at short sample of transcription file in French.
For more informations about XML, look at W3C technical reports or e.g. at Robin Cover's SGML/XML Web Page
Link to other tools and formats
Mark Liberman, Steven Bird and Terri Lander from LDC maintain a very complete page about tools and formats for linguistic annotations; please have a look there for a more global discussion about formats and a short description of various transcription tools and projects.