I've found the @-directories to be a kludge (e.g. public/private, what's that?) that is best forgotten. In the most recient versions (since 2007b, I believe), the best way to organize your classes is with packages. This gives a much cleaner namespace. I think working with the entire class in one file makes it a lot easier to get a sense of what the class is doing, and 1000% less annoying when it comes to refactoring (imagine changing 8 files after changing a variable name).
