Compiled by Valentin Spirik:
annodex http://www.annodex.net/ offers "Open standards for annotating and indexing networked media". Available as a Firefox extension.
syncVUE http://www.syncvue.com/ "makes the review and approval process easier than ever before. Multiple people can simultaneously view and annotate local copies of the same media files in perfect sync from different locations - whether separated by cubicles, city blocks, or continents." Commercial software.
Annotation Edit http://www.zeitanker.com/ "gives you a sophistcated interface to attribute and subtitle video or audio in very short time". Commercial software.
Belle Nuit Subtitler http://www.belle-nuit.com/subtitler/index.html is a "program to spot, edit and render subtitles for video editing, DVD authoring and digital cinema". Commercial software.
For research see also On the BBC Annotatable Audio project... (www.plasticbag.org, 18.10.05)