I am starting a Honeycomb application that will have a basic two panel layout, one panel on the left for the menu and one on the right for the main functionality of each section.
Contrary to the available samples of the Fragments API the content displayed on the right panel consists of a completely different UI for each of the menu options.
It is tempting to just replace the right fragment according to the selected section, but this would mean using just one activity in the entire app, and this does not sound good. Moreover, the fragment's lifecycle is tied to the activity, so no fragments will be killed until the activity gets killed, resulting in a lot of fragments "alive".
However, having a different activity with two panels for every menu option means that the fragment used for the menu will have to be added in EVERY activity and will be subject to inconsistent layouts across all the sections that should have a menu.
What are the best practices here?
This blog post summarizes the reasons for choosing fragments over activities:
Fragments are fairly new, so beyond that article, I'm not sure your going to find much for best practices. I think the decision you need to make is are my interactions tightly coupled and meant to share data or are they stand alone components which don't have much interaction.
edit, clarification: I think that using a single activity for an app isn't necessarily a bad decision. It's really a decision you should make based on the functionality of your app. Based on the article, an Activity is stand alone while a fragment is, typically, only relevant when combined with other fragments in the scope of an Activity. The situation you describe, with combinations of different activities is one of the pain points they designed Fragments to solve.