Cherrytree is one of those programmes that replaces a whole mess of other apps/programmes due to its versatility. I use it for all my writing/word processing needs - logbook, inventory, poetry, story/article/letter writing, address book/contacts list, recipe book, to do/task lists, project management, notebook, and much, much more. It's cross platform so I can use it on Windows or Linux without skipping a beat. I have yet to find a more useful, versatile programme.
Re: alternatives to PDF. I only use pdf if I absolutely have to and then only to read an already finished product that only comes in pdf format. My preferred format is RTF. Pretty well all word processors recognize rtf format. I have even made it the default for LibreOffice. That way the document can be read by any other word processor no matter the platform. I have yet to come across an issue where rtf cannot be read. (I haven't tried it on anything LaTex, yet.)