I was inspired by your question to create a plugin that I’ve been kicking the can on for several months. I’m calling it Deprecation Checker. By default, it scans the plugin and theme directories (recursively) to find deprecated functions. The functions list is sourced directly from the WP deprecated files.
It then outputs a nice list including line number, file path, old function, and recommended function to use in its place.
There are a couple of filters to add custom paths and custom deprecated functions for your own uses. You can also turn off plugin/theme directory scanning easily.
You can download it here: http://coderrr.com/deprecation-checker/ (will be on WP.org soon)
Once activated, browse to the Tools administration menu.