I am a huge fan of just how easy it is to create tables in OneNote. I hope that you'll take a leaf out of Microsoft's book here, they do get some things right. When you're writing notes, speed is the key, so something that requires you to go to another application, or even use a menu is going to be a fail in my book.
Please add me to the list of people requesting sub-folders. The bottom line for me is that it is simply counter-intuitive to not have them. Users are used to the concept of sub-folders, whether in explorer, sharepoint, or whatever. Tags are great, and I know that they're all the rage these days and are hyped up by web 2.0, but it seems to me that forcing people down that way of thinking is not catering to how most users think.