I completely agree with the existing answers, especially regarding the usage of packages. Packages require a lot of discipline, documentation, and structure, which really help to enforce best practices (along with R CMD CHECK). You can also use the codetools package to help with this. Use the roxygen package for documentation.
Beyond that, I recommend that you not only vectorize your code, but more particularly, make every effort to vectorize your functions, meaning that you should be able to provide vector arguments and get vectors returned (even from things like database calls). That will really improve your code efficiency and clarity in the long run.
Lastly, I really like to use something like Sweave to organize my code into clear literate reproducible research whenever writing a report. Along with this I recommend using the cache package.
