Then I discovered that website based applications, despite being targeted at end-users does not qualify for Super User. If Super User is not meant to target End-Users then what exactly is the target for Super User?
First off, you can ask questions about web applications on webapps.stackexchange.com.
Our target is computer software or hardware that you own and control. Anything that belongs to you, runs on your machine, etc. Websites or web services are not computer software in that sense.
You can check our scope by visiting our Help Center, which also specifically mentions that questions about web services are off topic.
That being said, we do of course focus on end users (or power users) of computers, and your classification in general is not that off—except that there are more subtleties in how each of the sites defines their scope. For example, not every developer question is suitable for Stack Overflow, but might be more on topic for Programmers.
