Christian Tietze has started a page collecting the various software tools available for the implementation of the Zettelkasten method of note-taking, storage and retrieval. He is inviting contributions for suggestions and reviews. Access it here: Zettelkasten Note Archive Software.
Here is another example of a ConnectedText database for academic notes from Jamel Ostwald, although he in the end opted to stay with MS Access. It’s worth comparing the design of the database (or the underlying template for a topic) with some of the other designs mentioned here earlier, such as Brian Lennon’s setup, Steve Zeoli’s example, Glen Coulthard’s library project, or my template.