This is a list of some of the tools that I use on a regular basis that have come to be an essential part of my workflow.
I use LaTeX for typesetting, and MacVim for typing (here is my .vimrc). References are managed using Bibtex. I also use Bibdesk, which is a simple GUI frontend for Bibtex files.
Most papers are kept in private repositories on Bitbucket. My coauthors and I use Git to allow us to work remotely on a paper and merge our changes. If a coauthor is not comfortable with Git, papers are kept on Dropbox.
I keep abreast of the literature using Inoreader (an RSS feed reader) with subscriptions to about a dozen arXiv and journal feeds. I have a few alerts set up on Google Scholar, which I also use for finding specific papers. See my post on Searching the Scientific Literature.
Lately, I write most presentations in Keynote. I use Latexit to typeset equations and paste the resulting (vector) graphics onto slides. For drawn diagrams, I use Omnigraffle.
Most of my coding is done with MacVim, in Python or Fortran. I also use the following:
Matplotlib and VisClaw.