It looks like the people behind Docear had a look at my personal wishlist with some great new features (unfortunately one of these features is Windows only, see below). Most important, in my opinion, Docear now comes with Zotero support. This is really great news.
On Windows (or if you run one of the recommended pdf readers under Wine), it comes with much better PDF Reader support, with pdf’s being opened on the page of an annotation. Moreover, annotations from RepliGo, an Android pdf reader, can also be imported by Docear.
See here for a overview of all new features and improvements.