That sounds like an excellent idea, but somewhat tangential to the issue of seperate applications.
If I understand what you are suggesting correctly, the system you are looking for would be able to construct arbitary assosiations between different resources. For example, you might set up relationships saying these webpages are related to this email which is part of this project, or that this document needs to be edited in the next five days, before this scheduled meeting using information in these three other documents, this folder of email and the sections that I annotated on this web page. Correct? If so, the Mozilla framework is probably an excellent place to implement such an application, since (as far as I can tell), it would be an ideal use of RDF which is well supported inside Mozilla. The application could create it's own RDF file contatining relationships between pieces of data and whatever metadata is required, whilst the data itself would be held in the files belonging to whatever external application created them.
As far as I can tell, quite a lot of the framework for this already exists within Mozilla. Some of the links from http://www.mozilla.org/rdf/doc/ describe quite similar ideas.
The neat thing about having this in a setting where everything is componentised is the extra flexibility that is avaliable. For example, it is probably true that a web browser can be totally seperate from such a proposed information managment application. On the other hand, it might be beneficial to integrate some email functionality directly into the application - the ability to retreive new mail and apply the adaptive or keyword filters that are avaliable in thunderbird. Composing a message on the other hand will always need a new window and so it doesn't matter if that is part of a seperate application. It's a similar situation with calendar (or any other scheduling app that integrates with the application) - if the calendar window itself is a seperate application, it doesn't matter, so long as the data from calendar is avaliable for use. It also means that people who don't need this functionality (like most home users, public internet access points, etc.)aren't burdened with an interface desigened around it.
As an aside, if anyone knows of a really good resource for learning about RDF, I'd really like to know about it.