PubCleaner is a tiny Windows app that very simply deletes all *.pobi periodicals from your Kindle except the most recent one of each publication. Warning: it is very early in development!
Download/Run PubCleaner 0.2.0 (ClickOnce, 6 KB loader) -- Note: this app is not yet signed, so Windows may prevent you from running it. You may have to choose "run anyway" after it downloads the first time.
PubCleaner project page on GitHub