There are usually both levels of division present. From the top, there are deployment units. These are named 'logically' (in your terms, think Eclipse features). Inside deployment unit, you have functional division of packages (think Eclipse plugins).
For example, feature is com.feature, and it consists of com.feature.client, com.feature.core and com.feature.ui plugins. Inside plugins, I have very little division to other packages, although that's not unusual too.
Update: Btw, there is great talk by Juergen Hoeller about code organization at InfoQ: http://www.infoq.com/presentations/code-organization-large-projects. Juergen is one of architects of Spring, and knows a lot about this stuff.
