The best Web project experiences I've witnessed are when people, whether they are designers, technologists, or IAs, know their field cold, know how to quickly and directly apply fixes and solutions, and have a willingness to work together toward a defined goal. IA is different for each one of these kinds of sites. Many of the IA differences hinge on who uses each kind of site, in what ways, and for what kinds of tasks. One of the recurring IA topics related to this question is labeling. Intranets and extranets have a more narrow and specified user base.
Users tend to familiarize themselves with a site more than users of an internet site do.
Quite oppositely, internet sites have to come up with a naming scheme that supports a variable, unknown, and constantly global group of users who may only visit the site once. To make things more difficult, there are other challenges. With intranets, the labels cannot be rooted in jargon or too tied to specific departments that mean little to employees beyond them. Each environment requires a different labeling schema, predicated on the context of users' behaviors and expectations. I haven't read much about IA for web applications, auction systems, or registration forms.