Draw On Screen Live

It seems such a tool exists for GNU/Linux already. It's called Ardesia. Read about it here

Example (taken from the above link):

Also, note that ardesia seems to have made its way into the repos (it's in the Debian stable repos, at least).

Pylote

Here's another one, Pylote. It's a Python based app.

                          

Compiz Annotate Plugin

There's also this plugin to Compiz, simply called Annotate.

Gromit

This is another option, which is in the repos, at least on Ubuntu. It's called Grommit.

   

You can use Gromit-MPX, which is an improved version of Gromit. Since it allows (but not requires) compositing, it should be much faster than Gromit where a compositing X11 desktop is available.

It's available in the Debian / Ubuntu repos at least. See my related answer over at askubuntu.com StackExchange for installation and usage under Ubuntu. (In short: use Pause instead of F9 under Ubuntu.)