I have been doing PHP stuff for almost one year and I have never used the function eval() though I know the usage of it.
But I found many questions about it in
A command line php shell is a great example. I guess you could fork the actual php code and write your shell extensions in C instead, but it seems much more sensible to do it in php. Since the person providing the code should already have full access to the system, there's no security issue at all. Once you get php compiled with readline, this sort of thing is actually really useful.
Drupal (optionally) uses eval to allow for ready extensibility. To accomplish this it takes user (generally administrator-only) input of code to be evaluated and stores it in the database. Drupal also has lots of people making sure that there are no security holes.