Which program to use to take notes?

The answer is: Xournal.
You can download Xournal with synaptic package manage. After installing it will be in the programs / tools menu.

(Note that I'm using hungarian ubuntu, so I'm just trying to translate the menu names :-))

To make the eraser tip to work go to the Options menu, and activate the "Eraser tip" option.
To make the pen button work as a highlighter go to the Options menu and choose highlighter in Button2 Mapping submenu.
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Installing Xournal:

You have to download these packages through Synaptic Package Manager before doing anything:

• libgnomecanvas2-dev
• libgnomeprint2.2-dev
• libgnomeprintui2.2-dev
• autoconf
• automake
• xpdf

... and dependancies.

Compilation and Installation

Download the Xournal distribution tar.gz file, and unpack it. (it will be a folder)

Go to the folder in the Terminal and type:

sudo ./install-binary

(and upgrade GTK+ and the other libraries if needed).

Then type:

./autogen.sh
make
sudo make install
sudo make desktop-install

Configure error message:
If autogen.sh generates the error message configure: error: Library requirements (gtk+-2.0 >= 2.4.0 libgnomecanvas-2.0 >= 2.4.0 libgnomeprintui-2.2 >= 2.0.0) not met even though you have sufficiently recent versions of these libraries on your system, then you need to install some missing development packages.