The logical thing to do is save and submit stories in HTML format. MS Word does of course have a Save As option for HTML. It is however every bit as messy and cluttered as one would expect from MS. As a HTML purist, I find it truly ghastly!

As for writing tools, I recommend the oddly named Yeah Write! It was designed by former Word Perfect owners/developers. It's basic in some areas. It won't do stuff like MS Word's grammar checking, but for pure word bashing and document handling, i.e. organising your chapters, stories, characters etc. it is unlivewithoutable. Good karma! Oh, and it produces clean HTML as its native format. Another Oh... and there's a free version too.