Which menu should a third-party module choose, between "Structure" and "Configuration"?
This and many other D7UX related things are best explained in the UI Patterns session from yoroy and Bohjan: Drupal 7: Interface patterns.

In short, Structure is meant for structural things which are used regularly (mostly during site building). If those modules add their stuff their and are not Views, Panels or similar, chances are that they are doing it wrong. :)

Not everyone exactly agrees on the IA (Information Architecture) of Drupal 7 yet or simply doesn't know about it. Not even Drupal 7 core is very consistent IMHO; I don't think the contact.module settings belong to Structure, for example, when not even those from path.module are, which are most likely way more often used.