This an extremely useful plugin, but with one major caveat.
I make full use of all of PHP 5.3's more powerful features - like closures (which I generally use to load files in hook callbacks). The problem is, if you use a closure while running this plugin, it completely breaks WordPress (as in, you get a fatal error and have to delete the plugin to get WordPress working again).
The reason is the plugin's use of the serialize() function. Unfortunately, PHP does not allow for closures ("anonymous functions") to be serialized. You'll get the error "Serialization of 'Closure' is not allowed"...