Where is the blacklist?

Nope, there isn't a blacklist implemented in the indicator. The panel applet supports filtering by appname (and actually more general regular expressions but that isn't exposed). In the panel applet this occurs in the dbus message filter, which in the indicator is in dbus-spy.c. It basically just looks at the notification and discards if it matches the filter instead of sending the signal.

On the other hand there is some filtering on the other side of the callback. Before adding the notification to the menu in message_received_cb in indicator-notifications.c, it is checked to see if it has a private hint ( which usually indicates a volume/brightness notification) or it is empty. This avoids cluttering the menu with useless notifications That do not contain any information.

Filtering by appname is what I want to do. I don't want the notifications from NetworkManager in the notification center.
So, if I understand this correctly, I have to add the application names in the source code and compile it?

Yes, you'd have to modify it somehow. Easiest would be a simple gstrcmp0 in the message callback, slightly nicer would be to add a gsettings key with a list of strings, load those into a hash table on startup and test the appname for membership.

I added support for the application name blacklist to the latest saucy package, you can see the usage in this question: https://answers.launchpad.net/recent-notifications/+question/242111