I have used Annozilla and other Annotea clients for annotating web pages and media with comments, tags and links to other resources. None of the Annotea-based clients that I have used have supported annotating OWL XML directly within the browser, however there is nothing in the Annotea draft that precludes annotating XML : you could use an existing Annotea server and modify one of the clients to support this.

My colleagues have produced an open source annotation server and set of bookmarklets that are based on Annotea, available here: http://sourceforge.net/projects/metadata-net/files/ However, the queries that be constructed over the annotations are limited to a fixed set including by URI, creator, date, language: the server does not expose a SPARQL endpoint.

Well, they are currently not, but they will be ;-) the ones elaborated in the context of the INSEMTIVES EU funded project: http://www.insemtives.eu/ Maybe you would like to have a look at it.

For the online/domain-agnostic case I'd give Knoodl a try, for or offline/text GATE is a good choice, and in case of domain-specific solutions (e.g. for audio, for images, etc.) you may need to look into the respective communities (such as sClippy for publications).

There is text mining based semantic annotators on the market already, which supply RDF annotations with linked data references to freebase and dbpedia, Nstein and Calais are among the leaders.