About the only open source annotation software I've seen is Apollo, which you can get (along with a ton of other stuff) from
GMOD . I've never used Apollo (I work at Celera so I use their stuff) but from the description it looks to be useful. It came out of the Berkley Drosophila group so a lot of the documentation is fly centric but if you read a bit further you'll find you can point it at the Sanger Center's databases.
