Is there a generally accepted format for submitting papers to journals?
The policies vary entirely from journal to journal about what is considered acceptable. APS journals, for instance, will accept both MS Word-based documents as well as documents formatted with RevTeX, their modified template system. ACS journals and a number of other publishers also offer their own LaTeX- and Word-specific templates for authors to use. Whether the use of the template is required or merely recommended is also a function of the journal. So, as a general rule, you should always check the homepage of a journal before you start preparing an article for submission to that journal. 

To some extent, I prefer working with LaTeX in preparing manuscripts, for the simple reason that their plain-text document format makes it a lot less painful to switch back and forth between different templates, compared to a word-processing format like Word or LibreOffice or Pages.