+1 for OneNote. I am not a fan of it but for vague education tools, the ones I've often heard are:
Diigo for collaboration/web annotation and OneNote for notetaking.
There's also the Live Scribe Pen.
In reality - it's just hard to imagine what students would want. There's no study on it and it often times could fall down to what the university or the service would offer for free.
Some others are:
http://www.aquaminds.com/nsDesktopProduct.jsp#
http://www.wiznotes.com/NoteTakingSoftware/tabid/36/Default.aspx
http://www.techsupportalert.com/best-free-notes-organizer.htm
...and of course some of the more staple "advanced" one of a kind notetakers: TiddlyWiki, Tree Sheets, Sticky Notes software, InfoQube, Microsoft DreamSpark, Bibliographical software like Citavi, Noteliner, PersonalBrain, MindManager, Outliner4d, Rainlendar, WriteMonkey, Pigeonhole, Anki, CintaNotes (Evernote Clone)...but I end up dropping those except for the last four so I can't really speak for how someone with a heavier load would be productive from these.
The few ones I use that can be substantiated to something close to educational are Goalscape and Compendium and both of those aren't popular with majority of notetakers.
Compendium
because it's used by NASA and Goalscape because it's used
by someone who competes in athletics.For websites, I assume some of these might be of use:
http://debatewise.com/
http://www.truthmapping.com/
http://www.licorize.com
http://www.42goals.com
Google Docs Cloud Storage Plug-inhttp://www.zoho.com
http://www.posterous.com
http://www.recallplus.com/index.php
http://www.ustream.tv/
http://www1.teachertube.com/
http://yourschoollive.com/
http://www.openblackbelt.com/
http://www.frobee.com/slideshow-maker/
http://www.announceschool.com/
http://www.agentanything.com/
http://openstudy.com/
http://www.ask.metafilter.com
http://www.quora.com
http://www.noteutopia.com/
http://class.io/
http://www.31projects.com/
http://www.sweetsearch.com/
(I'm forgetting a link but it's basically an online website that functions like PersonalBrain)
mahesh2k, are you aware of DC's earlier mega-thread General brainstorming for Note-taking software, started by superboyac? 34 pages and counting.
I assume he is. That's why he's making a filtered topic out of that mega-thread. At least this is how I interpret this thread.