Yeah, the way comments stack up and nest on GoNintendo can be confusing. How I handle it is to put my cursor right next to the dividing line for the comment and then scroll up. If my cursor scrapes by another dividing line, it means the reply wasn't in reply to that comment. When my cursor hits a particular comment, it means it was in reply to that particular comment.

Wow, that's a very convoluted way to explain it. I blame the fact English isn't my native language. But it's actually a very simple, easy and quick trick to find out to which comment the reply belongs, as long as my explanation is understandable enough