Except for the gui (by which I assume you mean wysiwyg) Emacs with Org-mode meets these requirements, albeit requires a bit of configuring and a couple add-ons. It takes a bit of learning, though, and wouldn't meet a user-friendly requirement. Org-mode does meet a few wysiwyg items (font size, underlining, italics, etc.) but certainly isn't full wysiwyg solution. Still, it's probably a better solution than LaTeX, because (1) Org documents can be seamlessly exported to LaTeX (and many other formats), (2) Org documents tend to have much cleaner (or even no markup) compared to LaTeX, and (3) add-ons extending functionality can be easily crafted in Emacs.

To get an idea of what you can do in Orgmode, a good place to check is the books/publications linked on John Kitchin's page. He's a professor of chemistry who uses Orgmode for lots of different things. Among other things (and also listed on the linked page), he is the author of the org-ref extension that integrates citations and referencing into Orgmode, using the bibtex database:

http://kitchingroup.cheme.cmu.edu/blog/2014/08/08/What-we-ar...

Here is a youtube video demonstrating use of the org-ref extension for citations and references:

https://www.youtube.com/watch?v=JyvpSVl4_dg

Thanks for this.

1. Latex does all of this. 2. Latex is user friendly....seriously. have you used latex for anything? Latex is incredibly easy to learn.