A lot of markdown note apps including FSNotes (https://fsnot.es) support the TextBundle (http://textbundle.org) format so you can embed images in the same document.

HTML is nice for more advanced documents, but I prefer note taking in markdown as it's a simpler syntax, even when viewed in raw text.

I think HTML is perfect for this app because it's more for academic use and less personal use like grocery/todo lists, reminders, etc.

Having a synced mobile version is crucial as you want to access your notes on the go right? (at the grocery store, etc.)