EDIT:

Option 1 (compiz composite manager)

As far as I read about the ink over apps application... you can try with the "Annotate" plugin in compiz.

1) Intall the compizconfig-settings-manager, compiz-plugins and the compiz-plugins-extra packages running code below.

sudo apt-get install compizconfig-settings-manager compiz-plugins compiz-plugins-extra

2) Open the compizconfig-settings-manager application.

3) Go to the "Extras" category and enable the "Annotate" plugin.

4) Click in the plugin to view and set the configuration.

5. configure the plugin according to your needs.. here you have an example.

You can launch whatever application, draw in it and use the shorcuts for the gnome-screenshot app like Alt + Print to take the screenshot of the windows you drew.

Option 2 (with any composite manager eg: xfce, compiz, xcompmgr etc)

Another software to draw over the desktop is Ardesia.

Ardesia is the free digital sketchpad software that help you to make
coloured free-hand annotations with digital ink everywhere, record
them and share on the network. It is easy to use and impressively fast
and reactive. You can draw upon the desktop or import an image and
annotate it and redistribute your work to the world. Let's create
quick sketch and artwork.

1) To install Ardesia, open a Terminal and type:

• sudo apt-get install ardesia

2) To open the app eg: Xubuntu.

Go to Menu > Accessories > Ardesia Desktop Sketchpad

3) You can draw over and app or your desktop and you can take screenshots with the Ardesia toolbar.

Option 2.5

If you have a slow computer, you might want to try option 2 using lxde and xcompmgr (a lightweight composite manager)

To run lxde and xcompmgr,

1) Install both programs

sudo apt-get install lxde xcompmgr

2) follow the instructions at How to start applications such as xcompmgr at start up? to get xcompmgr to start in lxde

This option works rather well, even on slow computers.

Option 3 (without composite manager)

Another application to draw but without a composite manager is Pylote.

Pylote is a software making it possible to draw on the screen of the
computer, like handling various instruments of geometry. It is a
software multiplateforme, free (license GNU GPL), made in Python
(computer programming language) and PyQt4 (or PySide) for the
graphical interface.

To run Pylote you need first python (greater than or equal to 2.6) installed by default in Ubuntu, and python-qt4.

1) Open a Terminal window and type:

• sudo apt-get install python-qt4

2) Download the pylote.tar.gz file. (Pylote install GNU / Linux)

3) uncompress the tar.gz file

• tar xvzf /path/to/pylote.tar.gz

4) Enter in the pylote folder and make sure the file pylote.pyw has execute perms.

• cd /path/to/folder/pylote

  
  



• chmod 755 pylote.pyw

  
  

5) Run the pylote app with double click in the pylote.pyw file

6) Take an screenshot after drawing over an app or your desktop. eg: scrot

• sudo apt-get install scrot

Then you can hit Alt+F2 and type

• scrot -s /path/to/your/screenshot.jpg

with the -s option you can select the area to take the screenshot and save at .jpg.

Hope this will helpful.