I thought about this awhile ago and it recently resurfaced as my shop is doing its first real Java web app.
As an intro, I see two main package naming strategies. (To be clear, I'm not referring to the whole 'domain.company.project' part of this, I'm talking about the package convention beneath that.) Anyway, the package naming conventions that I see are as follows:
Functional: Naming your packages according to their function architecturally rather than their identity according to the business domain. Another term for this might be naming according to 'layer'. So, you'd have a *.ui package and a *.domain package and a *.orm package. Your packages are horizontal slices rather than vertical.
This is much more common than logical naming. In fact, I don't believe I've ever seen or heard of a project that does this. This of course makes me leery (sort of like thinking that you've come up with a solution to an NP problem) as I'm not terribly smart and I assume everyone must have great reasons for doing it the way they do. On the other hand, I'm not opposed to people just missing the elephant in the room and I've never heard a an actual argument for doing package naming this way. It just seems to be the de facto standard.
Logical: Naming your packages according to their business domain identity and putting every class that has to do with that vertical slice of functionality into that package.
I have never seen or heard of this, as I mentioned before, but it makes a ton of sense to me.
I tend to approach systems vertically rather than horizontally. I want to go in and develop the Order Processing system, not the data access layer. Obviously, there's a good chance that I'll touch the data access layer in the development of that system, but the point is that I don't think of it that way. What this means, of course, is that when I receive a change order or want to implement some new feature, it'd be nice to not have to go fishing around in a bunch of packages in order to find all the related classes. Instead, I just look in the X package because what I'm doing has to do with X.
From a development standpoint, I see it as a major win to have your packages document your business domain rather than your architecture. I feel like the domain is almost always the part of the system that's harder to grok where as the system's architecture, especially at this point, is almost becoming mundane in its implementation. The fact that I can come to a system with this type of naming convention and instantly from the naming of the packages know that it deals with orders, customers, enterprises, products, etc. seems pretty darn handy.
It seems like this would allow you to take much better advantage of Java's access modifiers. This allows you to much more cleanly define interfaces into subsystems rather than into layers of the system. So if you have an orders subsystem that you want to be transparently persistent, you could in theory just never let anything else know that it's persistent by not having to create public interfaces to its persistence classes in the dao layer and instead packaging the dao class in with only the classes it deals with. Obviously, if you wanted to expose this functionality, you could provide an interface for it or make it public. It just seems like you lose a lot of this by having a vertical slice of your system's features split across multiple packages.
I suppose one disadvantage that I can see is that it does make ripping out layers a little bit more difficult. Instead of just deleting or renaming a package and then dropping a new one in place with an alternate technology, you have to go in and change all of the classes in all of the packages. However, I don't see this is a big deal. It may be from a lack of experience, but I have to imagine that the amount of times you swap out technologies pales in comparison to the amount of times you go in and edit vertical feature slices within your system.
So I guess the question then would go out to you, how do you name your packages and why? Please understand that I don't necessarily think that I've stumbled onto the golden goose or something here. I'm pretty new to all this with mostly academic experience. However, I can't spot the holes in my reasoning so I'm hoping you all can so that I can move on.
Thanks in advance!