When I write a paper, it begins as a largely creative processes where I'm trying to effectively convey my scientific contribution. By submission time, I feel like a typesetter tracking down TeX errors, fixing broken references, and changing my figures to f1.eps, f2.eps, etc. I find the typesetting aspect distracting and I put it off as long as possible.

I like to quickly hammer out a rough draft of a paper in a no-frills text editor. I like EverNote because it's easy to throw figures into the document, and since your note is on the cloud, you can work on your paper from any computer.

Once the paper is nearly done, I'll move it into a TeX document. I like to use TeXShop for Mac because it updates the PDF view of the paper with every compile. I use pdfTeX since I've found it's easier to throw in different sorts of files (.jpg, .png, .pdf). I also like to have these packages in the preamble.

\usepackage{\ensuremath}   % user-defined commands will be typeset in math-mode in text- and math-mode.
\usepackage{\xspace}       % intelligently puts spaces after mathmode.
\usepackage[T1]{fontenc}   % greater-than and less-than symbols don't turn into upside-down question marks

% For example:
\newcommand{\Rsun}{\ensuremath{R_{\odot}}\xspace}            
%\Rsun Gives the right symbol in text and math-mode.               

I track the TeX source documents (.tex & .bib) and all figures with. The

git diff --color-words

command shows the specific words (not just the lines that were changed).

I use BibDesk to manage my references. It's pretty easy to import the bibTeX citation directly from ADS into BibDesk.

http://bibdesk.sourceforge.net/

This obviously depends on how savvy your collaborators are. I'll email a .zip file of my TeX source to my collaborators and instruct them to edit the TeX source directly, reminding them that I've got version control running so I'll see all their changes. I'm keeping an eye on the ShareLaTeX product. It promisses to make working collaboratively on a TeX doc like a working on a Google doc. I'm not quite ready to use it yet, but I think it has promise.

https://www.sharelatex.com/