I would recommend that after Tafsir (commentary) is implemented in Zekr, adding an integrated editor for creating our own notes/commentaries/etc would be great. For reference, we can see how it's implemented in e-Sword http://www.e-sword.net/features.html or see my attachment.
The Study Notes is used for creating our own commentary for any ayah of the Qur'an while The Topic Notes is for creating works based upon a topic, not tied to a specific ayah. While not mandatory, it would be very nice if we can add formating to the notes. Ability to add hyperlinks to any ayah is also highly recommended, for example in the Notes we type "baqarah:12" or "2:12", then we block the text, then we hit the button "Insert Hyperlink", the text would be converted into a hyperlink to Surat Al-Baqarah ayah 12. When we click the hyperlink of course it would move us to the ayah, but if we only move the mouse cursor over the hyperlink, a tooltip comes up showing the full text of the ayah and the translation.
We should be able to save the notes and easily share the notes with other Zekr users. The Study Notes & Topic Notes should be placed on the same frame with the (upcoming) Commentaries, just on different tabs. Of course users can disable/enable the Notes.
IMHO this feature will greatly help users who seriously studying the Qur'an or writing a book/essay/etc about the Qur'an or maybe want to share his'her notes on his/her blog/website so that everyone can download the notes and add it in their Zekr.
Kudos to all the contributors, may Allah rewards you for your good works!