Various things that I found invaluable during my research.

Mac OS X Software

Best described as an iTunes for academic papers. It allows you to store and organise PDF files and export bibliography lists for use in LaTeX, etc. It's not free, but well worth the price (especially with the student discount).

Package manager that allows you to easily install most linux programs on your Mac.

Similar to Fink (with only slightly different ported programs and versions). Can be a pain to get Fink and MacPorts working on one machine, so it's probably best to pick one and stick with it.

Handy Mac FTP gui. Not free, but the University of Cambridge has a license that covers staff and students.

Cool little program that turns a MacBook's sudden motion sensor into a three component seismometer and displays data on the screen. Very useful for educational purposes!

When the time comes to write up, MacTeX allows you to compile your dissertation LaTeX files into a beautifully presented form, right at home on your Mac. Default install includes TeXShop.

More than just a text editor: TeXShop allows you to locate a sentence in your TeX file by clicking in the PDF output and vice versa. Included in MacTex.

Free text editor for coding, scripting, web design and much more.

Other Software

Hugely useful for backing up PhD dissertations, paper submissions and seamlessly transferring files between multiple computers, whether they're Linux, Windows, Macintosh, mobile...

Wonderful little linux tool for easily and accurately extracting data from graphs, such as those in academic papers. Can be installed via Fink or MacPorts.

It's probably not possible to do research in seismology without using these mapping tools.

There's a reason this website looks familiar.

Cambridge weather
For when it's too much effort to check out the window.

I was sad to graduate.

Fun JavaScript plotting library, used to create the interactive seismometer map.

Allows you to connect to the university network remotely for accessing third party websites and other services. Very useful if you don't live in a college.