It might not even need an application to handle snippets.
jabref is very flexible and it is easy to add a file link within a bibliography reference that links to the snippet. That way you can easily open the snippet from the bibliography entry. You can't search the snippet from with jabref (yet) but I'll have a think about how that might be possible. As much as possible I would like to keep things integrated with my full bibliography manager.
In fact it might not be too hard at all. I think we could add a custom field for snippets to jabref and have a way to import/update that field from the snippets file in the PDF container folder. It should be possible to either create a custom import/export filter to keep the two in sync or create a script that does this. (The new version of jabref is going to have a plugin system that would make it easier for someone to create a java plugin that could integrate this more elegantly.)
Doing this would mean that it would be possible to use jabref to manage references and to do quite powerful searches (including searches of the snippets) and still have the ability to do searches on snippets directly on the iliad.
But, again, we need to be careful about what happens if the PDF is processed again, e.g. if it is read again at a later date, perhaps for a different purpose, and more text is marked-up. We'd need to keep track of existing snippets and not wipe out the categories that had been added externally. This is can be done, but means more work.