You might take a look at Notebooks for iPad. While I'm nowhere near the novel stage, all my writing is being done in that app at this point--essays, character sketches, short stories, ideas, and things like product reviews. Others who've used it say it's plenty versatile enough to use for a novel. Other notebooks I've created within the app contain everything from jewelry ideas to research on how to configure networks. Random recipes I've found on the web, bits of folklore I'm ransacking for story themes, and the plans for an upcoming bathroom renovation...everything has it's own notebook, most likely nested within other Notebooks that may be a mix of text notes, PDFs, web pages, or images.
The catch--like most of these apps--is that it doesn't support writing or editing of RTF text files, though you can import and read them. There's no real formatting possible with it at this time. That seems to be an Apple-limited issue; I've heard devs complain about it in a number of forums.
It's one of the apps I use daily in spite of the limitations, and it's been one of the better tools I've come across, well worth the money to me.