I've been struggling a little with Apigen myself (it used to generate an empty documentation), but in the end i got it working (on Windows) using the standalone edition at https://github.com/apigen/apigen/downloads.
(update: apigen can also be configured for Netbeans)
Unpack it for example at d:\apigen
Now find and rename apigen.neon.example to apigen.neon and open this neon config file in a standard text editor. You also need to fill in params as source and destination, if you want it to work with Netbeans.
Presumably you want to add the inc extension. So find the extensions:
line and change it to extensions: [php, inc]
Open the Windows command line interface (cmd.exe) and go to d:\apigen
Now run something like:
apigen --source e:\wamp\www\ --destination e:\apigen_output --config d:\apigen\apigen.neon
This should now generate your documentation.
In Netbeans (8.0), first go to Tools, options, PHP, frameworks & tools, apigen and set path to apigen.bat. Now right click your project, select properties, apigen, and select the configuration file from above. Then right click your project and click on Generate Documentation.
As another way of doing this, I've also seen people unzipping ApiGen in the PHP path like e:\wamp\bin\php\php5.5.12
Then, in Windows go to Computer > properties > advances system settings > (tab) advanced > environment variables. In the second list of system variables find path, click edit and add something like this to the end: ;E:\wamp\bin\php\php5.5.12\
Do not forget the semicolon.
Apigen should now be globally available from cmd.