What I like most about the Mac is that there is this enormous subculture of nifty productivity software. These programs tend to be more numerous, easier to use, and of better quality than those I have seen for other platforms. These days there are a lot of useful Web applications around as well. People have also started asking me what iPad apps I use. (OK they haven't, really, but I was just looking for a modest-sounding reason for why I'm going to tell you about what I like anyway.)
I enjoy trying out new software, so I'll try to keep this page regularly updated as I learn about new software and also about which shiny new programs I actually end up using day in and day out. Last update: 27 December 2016
Here is a list of software that I recommend. None of these are very expensive; many are free. Except where indicated, everything on this list is software that I use regularly.
For keeping research notes, I've gone through a bunch of different apps, but I have settled on Evernote. It is well suited for short notes that you want organized by date and by tag. It has an email-like interface with multiple panes. Probably its best feature is that it has excellent mobile apps that sync with the desktop version. Therefore I often use it for taking notes during talks. So if you saw me fiddling with my phone during your recent talk, either your talk was really boring and I was checking my email, or your talk was really interesting and I was taking notes.
Another cool choice is VoodooPad, which I used for several years. VoodooPad is essentially a personal Wiki, i.e., you can create new pages in your notebook to keep organised. But, unlike regular Wikis, it's easy to change formatting, copy and paste pdfs of graphs, etc. It's Mac-only.
You might also look at Yojimbo. It has good reviews, but I haven't had a chance to try it.
I am in love with Alfred (the computer program). It is an application launcher, which is a program that allows you to start applications anywhere on your machine using only a few keystrokes. You start the launcher with a hotkey (say, Cmd-Space), it comes up instantly, and you type in PPT. A menu comes up with all of your applications and documents that whose name (NOT contents, like Spotlight) contains "PPT". You could scroll through this list, but you don't need to, because it has been cunningly ordered so that PowerPoint is at the top. You press Enter, and PowerPoint launches. That's it. It took you more time to read this paragraph than it would have to find and run any application on your machine.
Alternatives: Quicksilver was a popular launcher that I used for many years, but these days it is slow and not really kept up to date. It was also never really documented, so learning to use it means reading a lot of breathless Lifehacker posts about how if you just click a checkbox three levels down in the preferences, hit Cmd-Ctrl-Shift-Space, and click your heels three times, QuickSilver will actually send a message to your IoT-enabled toaster to start cooking bread for you. Other launchers that I have heard of are as LaunchBar and Butler.
As for mail clients, the default client Mail.app is all right, but the keyboard shortcuts are crap and I got fed up with it for interacting poorly with the University IMAP server. After a long search, I have settled on MailMate, a lightweight but amazingly powerful and customizable client. Not for the fainthearted, but very effective.
For editing code, my favourite port of Emacs to OS X is Aquamacs Emacs. I have used several Aqua Emacs ports over the years, and this is hands-down the most Mac-like. For a while I used TextMate, which is also very well-done; it has many powerful Emacs-like figures, but in a fully Mac-like package. Its interface for multi-file projects is significantly better than Emacs. But in the end I decided that I wanted Emacs. (I'm not fussy about editors, I switch back and forth between Emacs and vi every day.)
I have recently discovered that Apple's Pages looks like an excellent tool for making scientific posters. I had been looking for a good tool for YEARS that lacked the overkill factor of InDesign. I've only tried it for a simple A4 sign so far, but I'll post an update once I try it for a poster.
I use BibDesk to manage my BibTeX file. It has excellent support for pulling entries off of the Web (e.g., from Google Scholar). Alternatively, if all I have is a text citation, it also has a nice interface to highlight which text goes to which fields. The only thing it lacks is iPad support.
I am really liking Slack for group-local chat. It's basically IRC with really nice apps and really easy signup.
Having written all of the code for my dissertation in Java, my main advice for Java development is: Don't. It must be said, however, that the state of the art for Java development environments are better than perhaps any other high-level programming language. In this respect you can do no better than IntelliJ IDEA. I have only occasionally used Eclipse, but my impression is that Eclipse has most of the same features, but a significantly worse interface—and this is a real problem, because the whole point of an IDE is to get things done quickly.
Of course, for statistical computing and graphs, there is R. The latest Mac versions are quite nice.
You definitely want a package manager to allow you to download and build open source Unix tools easily. For example, this is a great way to get a TeX installation. You should know about MacPorts, a large repository of free Unix software that has been ported to OS X. An older alternative to MacPorts that people also used to use fink. These days, however, the cool kids are using homebrew. I'm not cool, so I just use MacPorts.
OmniGraffle is great for drawing graphical models and such.
I have recently been converted to the YNAB budgeting system. It's a well explained electronic version of the envelope budgeting system.
A common problem is how to get LaTeX equations into PowerPoint or KeyNote. Mostly I use LaTeXIt for this, which is pretty nice. For PowerPoint only, there is also TexPoint, which integrates directly into PowerPoint rather than being a separate application.
You should also become familiar with the presenter tools in Keynote or Powerpoint that show your time and next slide on the laptop display while your slide is sent to the projector. These are to die for.
I keep all my bookmarks in Pinboard. This is a social bookmarking site like del.icio.us, except that it is not social. Basically, it stores all of your bookmarks on a web site that you can access from all of your devices. I use web-based bookmarking rather than browser bookmarking because (a) a hierarchical foldering system is extremely cumbersome, (b) I can access my bookmarks from any device. Perhaps you are curious about my bookmarks?
TripIt is a slick way to organize your travel arrangement.
It parses the confirmation emails that you received from just about every travel site you use
and integrates them into a single itinerary. This way you can have all of my confirmation
numbers on the go, using the TripIt mobile app.
There is a very slick way to set up your account. Simply forward a confirmation
firstname.lastname@example.org and it will create an account
from your email address.
A lot of the iPad apps that I like are companions to either a desktop or a Web app that I use. This is probably because: (a) no one has done mobile Web apps well, and (b) the iPad platform hasn't figured out how to handle storage, (I don't mean that sarcastically; it's actually hard) so apps like to use the cloud.