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Check out "Notebook" from Circus Ponies. Available for Mac and iOS.

-jcr

Look at how others do it.

One of the few pieces of software I have bought, enjoyed and thanked myself for buying it many times is Circus Ponies Notebook.
http://www.circusponies.com/
They do a 30 day trial. I don't remember if there is any other DRM but I doubt it since I really don't like having DRM, phone home, etc.
I do use two other pieces of software that phone home on each launch without asking you (my firewall picks it up) which is extremely annoying. Don't do that.I tell people about them or consider buying more copies. The developer responds quickly and gives free updates.

I am also extremely happy with linode.com and they give free upgrades periodically. That is a different service, and I am quite against you forcing the user to be online or phoning home, but you can see the kind of enthusiasm and increased users you get from good service.

As for piracy, it happens. I would be against spending so much time on DRM that it jacks up the price. Figure it is free marketing and get on with it.

Circus Ponies' Notebook.app has had a very similar animation from the beginning and has been continuously available on the NeXT/OSX platform for about twenty years. It was announced for iPad on 2011-08-11, three months before Apple filed.

I personally use mindmapping software for notes during meetings. It allows for the information to flow naturally and be reorganized and regrouped quickly (i.e. during the lecture). You might need other stuff for diagrams but mind mapping is terrific. I use mindjet because I learned it a decade ago, but the market is much more competitive now and I would likely pick another brand today.

Notebook by circus pony (link) is specifically designed for what you want to do and I've heard good things about it.

If you have a Mac, I hear Notebook works well for all your requirements: http://www.circusponies.com/

• VoodooPad: An excellent WYSWIG Wiki-like notebook
  
• Circus Ponies NoteBook: A visually impressive note-taking app that looks like a real lab notebook.
  
• Hog Bay Notebook: Similar to the above, but lightweight and with IMHO superior outlining facilities.
  
• PersonalWiki : A desktop interface to the web-based ZWiki.
  
• Devonthink: A note/snippet/document management system, which includes semi-supervised classification algorithms.
  

What KDE needs is a freeform database along the lines of Infoselect or Ask Sam or Circus Ponies - Notebook... haven't seen any such for KDE or Gnome...

Or Circus Ponies Notebook, which I use.

Notebook
Notetaker

I can thoroughly recommend Circus Ponies Notebook. It's what I use for all my programming notes and other research notes.

It looks like a notebook. It works like an outliner. You can organize work page by page, or use long scrolling pages. It has dividers with tabs for different sections, and customizable page styles. It has highlighters and stickies for annotation. It sets up system-wide clipping services to let you pull snippets of information in from any application. And the best bit is that it automatically indexes everything you put in it at the back, builds a dynamic table of contents at the front, date-stamps every outline entry, and has super-fast search including search by highlighter color and search of stickies. It imports and exports XML and RTF.

But unfortunately for you, it's one of the many great reasons to get a Mac.