Zim

Zim is a similar note taking application with wiki like features. Zim supports rich text formatting, links between notes and to external resources, inline images and even LaTeX equations. It has a familiar 'notebook' layout with tabs.

Here is a quick screenshot demonstrating some of the features:

Zim is extendible using plugins - such as the LaTeX plugin. There are lots more. Here is the list of default plugins (you may need to install dependencies of some):

Calendar
Create Note (from command line for keyboard shortcuts etc.)
Diagram Editor (using graphviz)
Equation Editor (using LaTeX)
GNU R Plot Editor
Insert Screenshot (using scrot)
Insert Symbol
Link Map (using graphviz)
Spell Checker
Task List
Tray Icon (actually an application indicator)
Version Control (using bzr - this should make synchronisation and back up really easy)

The only feature it seems to be missing is Ubuntu One synchronisation like with Tomboy, however, if you use the default Notes directory (~/Notes), you can synchronise this over Ubuntu One, as your notes as held in files in this folder.

OneNote - Office Web Apps

OneNote is awesome, and no, there isn't a compatible version for Linux. BUT you can use Office Web Apps which is almost as awesome as OneNote :)

You need a Microsoft Live account to use it.

It is a Web App so it runs in a browser and works flawlessly from Ubuntu too :)

I know it is still Microsoft piece of work, but if one likes OneNote then should use OneNote.

Nixnote

I use Evernote. Sign up for a free or paid account on the website, then download the Nixnote client software.

It supports multiple clients (PC, Mac, Android, iDevice, Web), tagging, sharing, searching, rich text, inline attachments (pictures, music) and crucially (for me) To Do items. That way, I know from a meeting note if I have any actions outstanding, even weeks afterwards, because when I click on my saved search "To Do", it pops up all the notes that have uncompleted actions.

The collaboration element from OneNote isn't there, but I don't have any need for that anyway. I personally believe OneNote is overpriced and as usual for Microsoft, single-client only (although they support a web interface now). Also, it looks like the 2010 version is only available as part of 2010, while the 2007 was available stand alone for £80 retail.

Here's a picture of Nixnote in action.

Updates

Nixnote used to be called Nevernote.
Also worth checking out the excellent, native client Everpad.

RedNotebook

RedNotebook is a graphical diary and journal helping you keep track of notes and thoughts. It includes a calendar navigation, customizable templates, export functionality and word clouds. You can also format, tag and search your entries.

Basket Note Pads

I've always liked Basket. It's not as nice or polished as OneNote, but it lets you organize things hierarchically, group things together, embed media...etc.

It worked beautifully for me when I was in school.

KeepNote

The search for a good onenote alternative has occupied me for many months. Having tried all of the above I have settled for the moment on Keepnote (.org). While not as flashy as Onenote it has some advantages. I sync it to a cloud and as such, all my notes are accessible because they are html :)

Task Coach - Your friendly task manager

Task Coach is a simple open source todo manager to keep track of personal tasks and todo lists. It grew out of a frustration that most task managers do not provide facilities for composite tasks. Often, tasks and other things todo consist of several activities. Task Coach is designed to deal with composite tasks. In addition, it offers effort tracking, categories, and notes. Task Coach is available for Windows, Mac OS X, Linux, BSD, and iPhone and iPod Touch.