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This might sound like a daft idea, but Evernote covers a lot of these requirements, why re-invent the wheel, why not just link the Omni suite of products into something like Evernote.

Here are some of the features I would see in a Note Taking app:
- A database-type design like OmniFocus, that stores all of my notes in one place - Covered

- Syncing between iOS and Mac devices - Covered

- A way to structure and organize the storage of individual notebooks (so that I can have a year's worth of admin meetings in a folder for example) - Covered with notebooks and tags

- A "notebook" should be able to have structure to it, such as sections and tabs (look at Circus Ponies Notebook app on the Mac as an example that you could do better); Perhaps tables of contents; And I do like Circus Ponies Auto-Indexing features - More difficult but not required with Tags

- You should be able to create structured text, such as outlines and numbered outlines with auto styling (like OmniOutliner for iPad) - Semi covered

- But you should also be able to create free-form text; You should be able to quickly apply styles to text (like OmniOutliner for iPad) - Covered

- You should be able to do a quick finger sketch and simple diagramming - Not sure how easy it would be to amend later

- You should be able to create tables to hold structured data - Covered

- Tagging and search, obviously - Well and truly covered

- Simple To-Do's should be able to be created - Covered

- Ability to "highlight" text (like in iBooks) - Not sure

- Ability to send an item to OmniFocus Inbox would be killer - Not sure

- I like the ability to record audio and link the text that I type with the audio recording (but this would be lower on my initial needs) - Not sure