There are whole websites dedicated to answering these kinds of questions. However, for the kind of work I do as a computational scientist, I have found some favorites over the last seven years of using Mac OS X. From now on, my current favorites with brief rationale for each one will be posted on the tools page of this blog. That page has also been added to the navigation bar at the top.
Please let me know if your favorites differ from mine and why — there might be a better program out there that I’m missing out on!