*A few students have asked, so I wrote this in response. Sorry for the lack of links when it comes to various bits of software, but, the titles are all eminently findable through web searches.*
Increasingly, everything written starts in one of two places: Textmate or Scrivener. If I’m working in Scrivener, it means I’m writing prose. If I’m working Textmate, it usually means I am writing code or I am writing a one-off piece that I am going to e-mail to someone or, perhaps, dump into Nisus Writer Express and format to print — I also use NWE to format documents exported from Scrivener. I haven’t had much luck in generating RTFs, DOCs, or DOCX files that Word wants to read without crashing. And so, while Word is one option for writing structured document, it is increasingly not an option I pursue.
I also use Textmate to interact with a variety of dimensions of what I will call here simply the MacPorts stack that I lovingly maintain on my computer. Among its many layers are Python, LaTeX, and R.
I am less content with my software stack for visuals: I rely on Keynote for more than I should, and I haven’t yet explored iDraw as an alternative to OmniGraffle, which I have kept in my desk drawer for years and years but I find I use less and less as its development path slowly diverges from my use path. *Sigh.*
For quick number crunching, there is still nothing as good as Excel, which remains the most counter-intuitive charting application ever invented — why, goodness why, is it still easy to copy and paste data into Keynote to make a chart than to do anything in Excel. That noted, Excel remains more robust than Numbers, especially as Apple continues to oscillate on what it wants out of its office semi-suite. (Some readers will note that I make no mention of Pages here, and, for good reason, I just don’t have the confidence that Apple has any vision in this regard. None that I can discern anyway.)
When it comes to data collection, especially for web sources, I’m afraid two applications have replaced DevonThink here, which saddens me. When I want to capture things from the web, Evernote is just too easy, and it’s always there. And it syncs to my iOS devices, and they sync back, and I can get those notes almost anywhere, and I don’t have to do much of anything to make that happen.
For all the paper, or pseudo-paper in the form of PDFs, there is Papers (2). It is not the smoothest of experiences, but it takes managing all that stuff out of my hands, and off my mind, and that’s worth something. The iOS companion app is nowhere near GoodReader in terms of ease-of-use and functionality, but I remain hopeful.