My favorite applications for OS X

I've recently upgraded to the mid-2012 version of the MacBook Pro, which has given me a chance to completely install all my programs from scratch, as well as re-evaluate the applications I use. After significant research, here are the the applications that I have found extremely useful for Mac OS X, by category:


Productivity and Organization Tools:

• Evernote: great note-taking and web clipping utility that synchs with the web and across devices (including iPhone). Also check out Evernote Trunk for many additional, productivity-enhancing add-ons.
• Papers2: pdf organization program (costs ~$50 with student discount)
• 1Password: password manager (costs $50)
• Transmit: Mac OS X FTP client

Text Editors:

• Aquamacs: An editor for text, HTML, LaTeX, C++, Java, Python, R, Perl, Ruby, PHP, and other languages (I use this mostly for LaTeX and Python). Based on GNU Emacs platform. 
• TextWrangler: professional HTML and text editor (and for other languages).

Graphics:

• Seashore: open source image editor for Mac. It is simpler to use than GIMP because it seeks to provide basic image editing needs, not to replace professional image editing products.
• Gimp: GNU Image Manipulation Program that is great open-source replacement for Photoshop. Useful for photo retouching, image composition and image authoring.

Note: Gimp requires X11, an application that implements the X Window System. However, Apple no longer provides X11 support for Mountain Lion directly (as X11.app). However, one can download XQuartz, which is an open source version of X11 that runs on Mountain Lion and allows to run all X11-based applications in Mac OS X.

PDF Reader:

• Skim: PDF reader and note-taker. Integrates with Timestamper for Mac application developed for   recording timing of pdf (Beamer) slides during a lecture.

Music and Videos:

• Spotify: stream music for free.
• VLC: open source and cross-platform multimedia player.

Security:

• ClamXav: free virus checker for Mac OS X. Based upon open source ClamAV engine.

Developer Tools:

• XCode: Apple's developer environment. Includes GCC, the GNU Compiler Collection. I recommend using the Command Line Tools for XCode, which can be installed from within XCode using the "Downloads" pane within "Preferences". Command Line Tools provide UNIX-style development via Terminal by installing command line developer tools (as well as MAC OS X SDK frameworks). Note that these can be installed without installing XCode here.
• Homebrew: command line package manager for Mac OS X.