I've always been impressed by people who can sit in a talk or a class and, while taking notes, extract the meaning of what's being said, rather than just the words. Their notes may not record many of the words that pass by, but often use shapes, quick diagrams, and lines to illustrate concepts.
I expect that when Jayson Adams of Circus Ponies started to design, he had these talented notetakers in mind. I've long been fond of NoteBook, and I use it regularly, but mostly to maintain process lists, which are long outlines of how I perform certain complex tasks related to TidBITS or Take Control. When I'm releasing an ebook or running royalties, I always check my process lists to make sure I haven't forgotten anything. But these lists, critical though they are, are really just normal outlines, because that's largely what NoteBook 2.1 could do.
New Pages and Objects -- With NoteBook 3.0, however, Circus Ponies has completely rethought the concept of NoteBook's virtual page, such that outline-based Note pages have now been joined by Writing pages, on which you can enter free-form text like any normal word processor. NoteBook 3.0 also offers a special To Do page that's actually a Note page set up for a task list, and a special Cornell Note Taking page that's really a Writing page split into three sections (notes on the right, review questions on the left, and a summary at the bottom). Ironically, despite having graduated from Cornell more than 30 years after it was invented, this is the first I've heard of the Cornell Note Taking System.
Whether you're on an outline-based Note page or a free-form Writing page, NoteBook 3.0 continues to extend the concept of what can appear on a page beyond what was possible in 2.1. You can now add a wide variety of shapes and a collection of lines via controls in the toolbar. The controls take a little getting used to, since they're both menus that appear if you click-and-hold (you cannot just click and let up, as works with normal menus) and, once you've chosen the desired shape or line, a "well" from which you can drag an object to the actual page. If you don't want the toolbar showing, a Shapes menu offers another way of inserting shapes on the page. Once a shape or line appears, you can modify it by dragging its handles or working the inspector to change its color, fill, rotation, shadow, arrows, and so on. You can also add text note objects merely by double-clicking the page and typing; these too can be modified and positioned anywhere on the page.
More interesting for some will be NoteBook 3.0's new Ink toolbar item, which you must add from View > Customize Toolbar. You can click and hold the Ink icon to display a menu, or you can just click it to switch among Mouse, Sketch, and Write modes. Mouse mode is normal behavior, and lets you move all the objects around. In Sketch mode, however, you can click and drag to do freehand drawing on the page; each time you let up on the mouse button, you create another object. In Write mode, which is available only if you have a tablet with a stylus, NoteBook uses Apple's Inkwell technology to do handwriting recognition on what you've drawn. I wasn't able to test this, not having a tablet, but I could see the combination of NoteBook 3.0's new features and a tablet being a significant boon when taking notes in classes where diagrams are commonplace.
Layers and Stickies -- These objects float on a layer above the actual page, so you can move them around without affecting the text or outline underneath, but they stick with the underlying text if the page is a long one and you scroll down. I note that because you can also add sticky notes that look like the classic Post-it Notes and flags that mimic those sticky tabs that accountants put on tax returns to show you where to sign. Sticky notes and flags live on yet another layer which is not attached to the underlying text, so if you slap one of those on a page, it shows no matter how you scroll. That said, if you start dragging a sticky flag and then press the Option key, you can attach it to a particular cell in an outline, after which clicking the flag highlights the cell and the flag scrolls with the page.
In fact, if a sticky note or flag bleeds off the page, the off-page bit shows even if you navigate to another page in your notebook, and clicking the visible bit returns you to the sticky's page. This is, of course, exactly how sticky notes and flags work in real notebooks, and it's useful to have that functionality in virtual notebooks as well. If they prove too cluttering while you work, you can use the View > Stickies and Flags command to hide or show all the stickies.
Sticky notes and flags can contain text and even ink drawings, although I found that NoteBook sometimes got confused when I added ink to a sticky and wouldn't let me edit sticky notes or flags until I quit and relaunched.
It's worth noting that sticky notes and flags also act somewhat differently than shapes, lines, and text notes. Those three act like objects in a drawing program, so to delete them, you select them and press the Delete key. Sticky notes and flags, on the other hand, can be dragged around but not selected for deletion. Instead, to get rid of one, you drag it off the page entirely, at which point it disappears in a satisfying poof. If you can't drag a sticky note or flag, you're probably editing it, and you must click elsewhere on the page to stop editing before you can drag.
Improved Outlining -- I don't want to imply that NoteBook 3.0 has deprecated outlining, since nothing could be further from the truth. It was already a good outliner, and now it's better. For instance, you can set cell numbering on a per-cell basis, with numbers applying to that cell's descendants as well, and you can also set the cell spacing of different levels in an outline.
There's also a new option in the preferences to use the left and right arrow keys to initiate cell editing rather than to turn pages. You can now drag cells to move or copy them between pages, sections, and even different NoteBook files. And, in something I've been wanting for ages, you can now press Shift-Return to create a new cell above the current one, rather than below.
Other Enhancements -- It's worth reading through the What's New in 3.0 section of NoteBook's extensive online help, since it lists numerous additional changes and improvements, many of which are rather subtle. Some of the more interesting changes include:
At this point in time, there are many programs that are roughly similar to NoteBook in providing features for note taking, snippet management, outlining, task lists, and file holding. It would be impossible to compare NoteBook with all of them, but from what I've seen on cursory looks through the feature lists of other programs, NoteBook 3.0 does a good job at providing a wide range of features, though with a focus on note taking and information collection. If you're in need of a place to take notes, store information, and more, give NoteBook 3.0 a look.
Details -- Circus Ponies makes a  available as a 14.8 MB download. New copies of NoteBook 3.0 cost $49.95, $29.95 for academic users, or $99.95 for a 3-user family pack. Upgrades are free for anyone who purchased NoteBook 2.1 from Circus Ponies in 2008; use the  to get a new license key. For those who purchased a copy before 2008, or received it as part of a promotional bundle like MacHeist, upgrades cost $29.95.