These are my current favorite Mac OS X programs for my work, with reasons (where there are alternatives).

Web Browser:

Firefox — Firefox is available on all major computing platforms, has tons of extensions (now called “add-ons”) that I use regularly, and is generally standards-compliant. Add-ons I recommend are AdBlock Plus, NoScript, CookieCuller, Readeroo, ScribeFire, GreaseMonkey, FoxMarks bookmark synchronizer, and Tab Mix Plus.

E-Mail:

This one’s boring — I use the built-in Mail.app due to its great integration with the OS and good support in Quicksilver. Mainly the latter.

Application Launcher:

Quicksilver — I don’t know how I’d get around OS X without it. Actually, I do: slowly. It allows one to do things like select a file, pull up a contact from the Address Book, and mail the file to them, all without ever touching the mouse. It also launches applications, a minor feature compared to some of its others.

Notifier:

Growl — A customizable notifier. Rather than all of your programs popping up their own notifications, they can just send them to Growl and you can control their display in one place.

File Transfer:

Cyberduck — It used to have some major SFTP speed issues, prompting me to use Fugu. However, those issues have been fixed, and I find it more flexible and “with” modern things like Growl and Quicksilver.

Text Editor:

Carbon Emacs - The best text editor. Ever. (Vi users, please no flaming). As Neal Stephenson put it,

I use emacs, which might be thought of as a thermonuclear word processor. It was created by Richard Stallman; enough said. It is written in Lisp, which is the only computer language that is beautiful. It is colossal, and yet it only edits straight ASCII text files, which is to say, no fonts, no boldface, no underlining. In other words, the engineer-hours that, in the case of Microsoft Word, were devoted to features like mail merge, and the ability to embed feature-length motion pictures in corporate memoranda, were, in the case of emacs, focused with maniacal intensity on the deceptively simple-seeming problem of editing text. If you are a professional writer–i.e., if someone else is getting paid to worry about how your words are formatted and printed–emacs outshines all other editing software in approximately the same way that the noonday sun does the stars. It is not just bigger and brighter; it simply makes everything else vanish.

Also, if you get bored, it has Tetris and a pscyhotherapist built in, among other things. (esc-x tetris and esc-x doctor , respectively).

Diagramming:

OmniGraffle - The best graphics layout program I’ve ever used. I make everything from signs for my mailbox to four-foot-by-three-foot full-color conference posters with it, and it’s not too difficult to learn. No books necessary.

Notes / Planning:

Scrivener - A writing program made by a writer, you can collect just about any kind of reference material and write on virtual notecards. My first paper was organized and written almost entirely in Scrivener.

Instant Messaging and VoIP:

Skype and Adium - I prefer Skype for most things, as it has robust video and audio capabilities. Adium is useful for connecting to just about every other network, all at once, with a combined buddy list.

IRC:

X-Chat Aqua - A native Mac version of the UNIX classic. Integrates with Growl.

Math and Algorithms:

Scilab - An open-source Matlab clone. GNU Octave is perhaps a little nicer and more Matlab compatible in some ways, but Scilab has a GUI and doesn’t require a fancy packaging system to install.

UNIX Package System:

MacPorts - A BSD portage system with packages for Mac OS X. I’ve found MacPorts to have a better selection and better compatibility across versions of OS X than Fink. The downside is that MacPorts compiles the packages when you install them, whereas Fink uses binary installation packages.

Command-Line Tools

These tools are used entirely or primarily from the command-line interface. To try them out, fire up Terminal.app. Please do be careful, though, if you’re new to the command-line. You can do major damage quickly.

Screen

screen is a utility that lets you create multiple command-line sessions within a single terminal/connection. Furthermore, if you get disconnected from a screen session on a remote machine, it will keep running. You can reconnect by logging back into the machine and running screen -RAD. A full tutorial is available on Kuro5hin here. It is built into Mac OS X, and is also available on most UNIX systems. If it’s not installed on a given system, you can probably download it (from here) and install it in your home directory easily.