Vikas Rawal has an excellent guide up at Github for writing papers with Emacs and Org Mode. He takes a reproducible research tact so it’s a great resource for learning how to produce a paper with everything in a single file and all the tables and graphs produced automatically.
The guides takes a “from the beginning” approach so it’s fine for even those with limited or, perhaps, no Emacs experience. If you have even a little bit of Emacs under your belt you should have no problems at all. One of the points that Rawal makes is that you can spend more time figuring out LaTeX than you do actually writing the paper. Using Org Mode removes most of that friction and lets you to concentrate on your writing but still allows an escape into LaTeX for specialized tweaks.
It turns out that Emacs and Org Mode are almost everything you need. He recommends Pandoc for some conversions, TeXLive and BibTeX for producing LaTex, and, in his case, R and ESS to handle statistics. R is a good solution if you’re producing a lot of statistics but the techniques he describes works just as well with other languages if your needs are different. He doesn’t go into the details of R itself so its use as the example language is not distracting.
Even if you know only a little LaTeX (or, I suppose, none at all) you can follow his recipe and get good results. That’s a major benefit when you’re just starting and don’t want to hassle with LaTeX along with everything else. Even the amount of Org that he uses is minimal so by following his example you can be producing great looking papers without knowing much about LaTeX or even Org.
I really liked this guide and recommend it if you’re looking for a way to produce journal-quality papers.