Application Enhancer. APE is practically the name of the program. Full name is Application Enhancer.
That is made by Unsanity, the developers of system haxies. http://www.unsanity.com/haxies/ape
If I remember correctly, I can't remember where it was but if Apple knows APE is installed they wont touch your system if you have problems and need help (software wise).
Can Application Enhancer or its modules crash your system? Application Enhancer itself is not known to have ever caused a crash itself. However, APE modules potentially can crash individual applications if there is a bug in the module or in the application being modified (sometimes APE modules expose "hidden" bugs in the applications).
Does Application Enhancer slow down the system? Due to the fact that more code has to be loaded at the application launch time, Application Enhancer can increase the application launch time (usually in the range of 40-60 ms per Application Enhancer module loaded on a modern Mac).