There are several schools of thought when it comes to the brainstorming and organization process. My favorite, by far, is mind mapping. A mind map consists of a central idea or topic from which sub-topics radiate out. It's similar to an outline, but due to its non-linear nature it allows the thought process to expand without confinement. This method is excellent for developing ideas and works wonders for everything from organizing class and research notes to planning your spring break. Obviously, this post isn't going to be a mind mapping tutorial. Tony Buzan, the "father of mind mapping," has some good free videos on his site, and an Amazon search will provide plenty of literature on the topic.
Mind mapping is easy to accomplish on paper and makes a great tool for taking notes in class without pulling out the old laptop. Personally, I find that software-based mind maps flow much faster and are easier to work with because they don't require erasing and redrawing to move topics around. There are several great applications, ranging from free to fairly expensive. This is one case where you tend to get what you pay for, though, so if mind mapping seems to work for you, I'd recommend taking advantage of some student discounts.
Mind Mapping for free
There are two packages which I'd recommend on the free end of the spectrum. MindNode is a simple mind mapping application with a decent interface and a variety of output options. It doesn't do much else, but if you just want a quick, easy way to brainstorm ideas, it fits the bill. FreeMind, although uglier, offers many more options. It has a good set of keyboard shortcuts, which allows maps to build as quickly as you can move your fingers (or your brain, should it be slower than your fingers after an all-nighter). It offers several map modes and has great export options, including XML/XSLT for those who want complete flexibility (and know what to do with it). FreeMind is a popular enough application that its file format can be readily imported into most other applications, including some online tools such as MindMeister.
There are several major players in the commercial realm of mind mapping software. You've got XMIND, NovaMind, ConceptDraw MINDMAP and more. I'm not going to go over every one, but there's one that stands out for me: Mindjet MindManager. All of these apps provide excellent mind mapping tools, so it's the extra features which make them most worthwhile. MindManager provides the best integration with OS X, allowing hyperlinks to urls, files, emails and anything else which can create a link in OS X, AppleScript integration, Spotlight and Quick Look integration, export to many popular formats, outline mode, note attachments and more. Its mapping tools allow for a huge variety of aesthetic choices, and creating boundaries, relationships, callouts and other vital mind mapping tasks is a breeze. Many of the other programs which offer the same tools fail to integrate with the OS at the same level MindManager does. MindManager is $129US, which is likely a little steep for most students. Mindjet provides an academic purchasing program for students, faculty and non-profits. NovaMind has an Express version for $49US. With educational discount, you can pick up XMIND for $99.95US. Demos of all of these programs are available, so do a little comparison shopping if the mind mapping concept is appealing.
Another truly useful concept in note-taking and organization is the wiki. The idea behind a wiki is to have keywords within context link to definitions or related information (e.g. Wikipedia). It's a miniature, self-contained version of the web, with hyperlinks ensuring that everything is defined and associated with appropriate content. When used as a note-taking device, it allows for non-linear thought by letting tangents become their own pages. They're not as ideal for organizing and outlining a structured writing project, but they're great for collecting and organizing information in an intuitive manner.
You could set up your own wiki on a web server, use free online services like PBwiki or Zoho Wiki, or run web-based software like Nanoki or TiddlyWiki locally, but the setup can be complex, features can be limited and integration with your other tools is nearly non-existent. Fortunately, there are some great tools which don't require much setup or maintenance at all. For the most basic of wikis, check out WikityWidget. It's a Dashboard widget with a wiki system built into it. If you're a Quicksilver user, there's even a plugin for rapid entry of text into the widget. Unlocking the real potential of heavily-linked collections of documents, though, requires a little more firepower.
Some of the most powerful note-taking and organization tools incorporate wiki-style linking. DEVONnote (about $15US after the 25% educational discount), for example, offers a full set of features which include automatic wiki links, amongst other means of searching and organizing notes. It's a less-capable version of DEVONthink (comparison chart), which is worth looking at as well.
VoodooPad, which is essentially a personal wiki, is far and away my personal favorite app for wiki-style notes. I can't even begin to list all of its features in this article, but suffice to say that it excels at text editing, file and document linking (as well as attaching or embedding), and has very intelligent search capabilities. It's also highly extensible, with AppleScript support, built-in support for scripting in multiple languages and a plugin architecture. There's a free version available with a fairly limited (but highly useful) subset of features. For most student needs, the regular version ($29US) is an amazing tool for gathering notes, brainstorming and preparing to write papers and make presentations. The Pro version ($49.95US) adds several advanced features, such as document encryption, meta values for individual pages, a built-in web server and event triggers. If you need these features then it's worth the extra cash, but the standard version is perfect for the typical student.
Many of the other organizers (covered below) offer some form of document cross-linking. Additionally, there's a writing tool called Scrivener which I'll talk about in much more detail in the next installment. Scrivener is geared more toward the actual writing process, but I mention it now because it works well for taking and organizing notes and has the ability to create links within text to any other page in your document. As I said, I'll be going into more detail on Scrivener shortly, and Mellel fans can rest easy, too ... it's covered.
MindManager and other mind mapping programs, as well as some of the wiki-type applications (such as VoodooPad), make it easy to link external files to a topic. It's not always so easy to preview them or quickly get content out of them, though. That's where the organization programs come in. Most of these apps are powerful enough to be a complete solution for everything from taking and collecting notes to tracking references and documents, all in a highly-organized and easy-to-search environment.
I'll mention Papers first, because it fits into multiple categories. Geared toward scientific research, Papers is both a research tool and a document organizer. It has excellent, built-in tools for searching external repositories, importing links and PDF files and adding notes and additional information. A full-screen viewer and a gorgeous (award-winning) interface make dealing with scores of PDF files a pleasure.
As far as I know, Papers doesn't have built-in annotation tools, which I use frequently. Highlighting and calling out sections in my reference files, as well as adding my own notes, makes it a lot easier to find pertinent information in any PDF I've collected. This calls for a slight tangent ...
PDF annotation tangent: There are a few options for annotating PDF files. If you own Adobe Acrobat, you've already got an excellent set of annotation tools. There's no need for a bloated PDF application, though: Preview -- built into OS X -- has basically the same tools, loads faster and uses fewer system resources. To find these tools, open a PDF and look under the Tools menu for the Mark Up and Annotate submenus. If you use them frequently, right click on the window's toolbar and choose Customize Toolbar. From there you can drag the tools you like into your toolbar for easy access. I should also mention that Skim, an open source application for reading scientific papers, takes annotation a step further. In addition to the markup tools, it provides Spotlight-searchable indexes of your annotations and notes, including automatic indexing of text within areas you've highlighted or called out with the shape tools. It creates an extra file for each PDF with these indexes, which can throw off some organizers, but most deal just fine with the extra, Quick Look-friendly files.
General information organization
There are several applications which serve as general purpose repositories for notes of many types. Yojimbo ($39US) is powerful and quite popular, providing a database-driven information collection which handles multiple file types. Alternately, Together (also $39US) collects information in much the same manner, but rather than storing its collected documents, notes, images, etc. in a database, it keeps them right in the file system. The respective benefits of database versus file storage are the source of heated debate, one which I'm not getting into right now. Both programs offer Spotlight integration, file previews and tag-based organization.
I personally prefer Together for a few reasons, the main reason being that its close integration with the filesystem and ability to write tags out to Spotlight comments means that all of the information I've collected is easily searchable and usable without loading the application. It also handles more file types and uses Quick Look for previews, meaning that anything you can view from Finder, you can preview in Together. The ability to save web pages to PDFs was recently added, so grabbing information and annotating web content is a simple process. Together also provides hierarchical folders and file groups in addition to tagging and smart folders, allowing a variety of methods for organizing your files. Both programs can save web archives and bookmarks, the former being a great way to save information which is subject to disappearing or changing.
Another great application in this category is SOHO Notes ($39.99US). It, like Yojimbo, uses a database and provides excellent tools for storing, searching and linking files together. It adds some great tools, including the ability to scan papers and record audio notes directly into the database. Among its available note types is one called "Pages," which offers some word processing capabilities and full-screen editing. Like Together, you can organize your notes with tags, smart folders and/or in a folder hierarchy. It offers excellent Spotlight integration which, in case you haven't noticed, is quite important to me and my personal workflow. One unique feature of SOHO notes is the ability to create "forms" which basically give you a customized means of entering data of any kind (e.g. passwords, class schedules, phone numbers off of napkins, etc.).
Along the same lines, Bento ($49US, small educational discount available) is a potential tool in this area. It's basically a lightweight, elegant and user-friendly database from FileMaker. It integrates with Address Book and iCal and provides all of the custom form creation you'd need to build a personalized data entry system. It can link files to projects, embed images and -- being a database -- provides many options for searching and sorting. While it serves well for project organization, it's not the ideal application (in my opinions) for the purpose of note taking and research organization.
The previously mentioned DEVONthink provides a slightly different method of organizing notes. Rather than directly tagging notes, it uses a classification system which, for the most part, can develop itself automatically (DEVON refers to it as Artificial Intelligence). The system uses a folder hierarchy within the app, but everything is stored in a database which is searchable by a variety of criteria. By building associations between files as they're added, it can make finding information related to the current topic quite simple. As far as features go, it's pretty packed ... Spotlight integration, web access to the database, Rich Text File creation and markup, and mail archiving, to name a few. DEVONthink integrates tightly with the DEVONagent (mentioned last time) for a full research and information organization system.
For the enterprising
If you're feeling a little more DIY (and somewhat technically savvy), it's relatively easy to create your own system (or extend an existing workflow) using tools you already have. You can build your own folder hierarchy in Finder, add tags in the Spotlight comments of files (by hand, using AppleScript or Automator, or by using one of the myriad programs which can write their tags out to Spotlight comments), and then group your files and notes across multiple folders using Spotlight and Smart Folders based on your tags. Most applications which do a good job of incorporating tagging use a user-defined prefix such as an ampersand or bullet to signify a tag in the Spotlight comments (e.g. "&research &biology"). This system allows Spotlight and Finder to work hand-in-hand with any program which uses it.
You can collect web pages by saving them as archives or printing to PDF and marking them up with Preview or Skim. You can add any type of file to this kind of system, and it's intrinsically Spotlight-searchable (by tags, content, date, etc.) and Quick Look-compatible. Of course, the metadata (i.e. the Spotlight comments storing your tags) can be easily lost if you're not careful, and you don't get some of the niceties of dedicated applications. It is, however, quite extensible and has a lot of possibilities. Because I personally use a system like this, I appreciate applications which are able to work in tandem with it, reading and writing the same tags and keeping my files universally accessible. If you do choose a primarily Spotlight-based system, you should definitely take a look at applications such as Leap, FileSpot and HoudahSpot.
This post covered a wide range of applications and I've concentrated on the ones I find the most useful ... which means there are a lot of apps that didn't get a mention. Feel free to pimp your favorite in the comments, and stay tuned for the "writing tools" roundup!