So, according to me, this is a big condition in the force.com stack that makes medium sized projects difficult, if not impractical. If you use managed packages in order to get a package prefix, it won't solve any problems, so it's not really worth the trouble.
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I try to organize a project into one level of namespaces. Instead of actual namespaces, you could give each would-be-namespace a 3-5 character name, to be used as a prefix. Any class which belongs in the 'namespace' gets prefixed.
Functional advantage of this type of convention is that it helps prevent name classes and clashes which are grouped by their 'namespace' when viewed in a sorted list, such as in an IDE, or Setup > Develop > Apex Classes
Sadly, several basic OO principles are still fundamentally broken. Apparently, the most important one is that every class forms an implicit dependency on each and every other class it has visibilty to, which is actually all of them.
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