Highly recommended apps are bolded. Also check out the blog posts about useful applications.
- DropBox - keep files synced over multiple machines and/or share files with others. blog post, related posts.
- Things ($40) or OmniFocus($50) - ToDo lists that are intuitively obvious and syncs with iPhone. blog post.
- 1Password ($40) - Password manager with browser integration and iPhone sync. Manages logins, identities, secure notes, software licenses, wallet items, and recently generated passwords.
- iWork or Microsoft Office X - or Open Office, NeoOffice, etc.
- PostView ($22) - Postscript viewer. (Much faster than Preview for postscript.)
- A package manager. Try Homebrew (blog post), MacPorts (blog post) or Fink.
- Time Out, Anti-RSI, or Awareness - Remind you to take ~10 second microbreaks every ~5 minutes and longer breaks every hour. It will annoy the hell out of you, but it's for the best. blog post. Awareness is less annoying and just sounds a chime when you've been working continuously for an hour. For Windows and Linux: Workrave.
- iTerm2 (donation) - give your Terminal app an upgrade (blog posts)
- StayFocusd- restricts the amount of time you can spend browsing time-wasting websites.
- Mailplane ($25, €21, £18) - Standalone app for Gmail. blog post.
- Sparrow ($9.99/€7.99/£5.99) - "The New Mail for Mac". Similar to Tweetie interface.
blog post discussing the top three
- TextMate ($50) - Can do everything TexShop can do and much more. Bundles for pretty much every programming language.
- Emacs - official Emacs which is now available in native mode for MacOS X (no X11 needed).
- AquaMacs - modified emacs for OS X.
- TexShop - Latex Only.
Paper Library Organization
- Papers ($42, €29) - iTunes like app for research papers. (blog post)
- BibDesk - Database to manages .bib file and organizes PDFs. Extensive "drag and drop" capability to add new references and to associate PDFs with existing entries. (blog posts)
- Mendeley - (blog post)
- arXivNow - an arXiv reader for Mac
Collaboration and Communication
- Google Docs - great for small group spreadsheets, documents, or presentations (blog posts)
Google Wave - threaded conversations for medium sized collaborations (blog post)
- The GraphicsMagick tools for converting, cropping, and much more are free and can be installed via MacPorts
- Graphic Converter ($35, €30) - Powerful image editing program. Converts PS/EPS to JPEG/GIF, crops images, and much, much more. Has all the basic image manipulation (but not creation) functionality of both Photoshop and Illustrator in one cheap application.
- Inkscape - Open Source vector graphics editor, with capabilities similar to Illustrator and CorelDraw. Excellent for making posters.
Electronic Research Notebooks
- EverNote - blog post
- MacJournal - use it to keep all your notes and thoughts in one place. It does cost money, but with a 15 day trial period there's plenty of time to decide if you like it or not.
- OS X Wiki Server - OS X server comes with a wiki server which can be used as an electronic research notebook
- Notational Velocity
- Disk Inventory X (free)/Grand Perspective (free)/Daisy Disk ($20) - keep track of disk usage
- Onyx - OnyX allows you to verify the Startup Disk and the structure of its System files, to run misc tasks of system maintenance, to configure some hidden parameters of the Finder, Dock, Dashboard, Exposé, Safari, Login window and of some of Apple's own applications, to delete caches, to remove a certain number of files and folders that may become cumbersome and more. (Some overlap in functionality with Secrets listed below in Tweaks.)
- USB Overdrive ($20) - Driver for mice and keyboards that lets you configure them either globally or on a per-application, per-device basis.
- Steer Mouse ($25) - Driver for USB and Bluetooth mice. You can customize buttons, wheels and cursor speed freely.
- Onyx - see above
- Secrets - Modify hidden preferences for the Finder, Terminal, Dock, and more. (Some overlap in functionality with Onyx listed above in Maintenance.)