There are 3 more real world lessons learned that should be mentioned here. These problems are not limited simply to web parts and related files. Items as simple as images and as complex site definitions (the blueprints that detail the creation of SharePoint sites) are all effected by improper non-WSP deployment. Site definitions, field types, event receivers, workflow, features all must be deployed via WSP. In addition CSS files, ASPX pages, and Master Pages will need to be deployed via WSP if they are to be used farm wide. As a general rule, if the item in question will affect the entire farm it will likely need to be deployed via WSP.

I have built quite some experience around Intranet, Extranet development using MOSS Publishing sites in large, globally managed environments. I have always felt that a mix between both would work best.