I use a great small app to rip DVD's and convert clips to my iPhone in superb quality, but the films I rip are just one long video,with no chapters. Is there an app that I can do this with on a PC?
yep theres Handbrake for Windows. rip a DVD with the iPhone preset.
but iPhones cant play DVD movies with menus and chapters i.e. DVD format (video_ts) so youll have to just have the whole movie.
but i think you can add chapter "markers" i.e. skip a certain amount of time like a chapter. check out the "Chapter" tab in Handbrake i think thats what you want and look at the documentation on handbrake.fr.