The Wall Street Journal ran an article (password-protected, alas) on June 16 titled "Marketers Promote Good Cookies", in which they discussed some of the challenges posed by these now-staples of Web-based software , as well as some associated solutions being considered.
If you are interested in how cookies work, to better appreciate this article and what it might mean for you, this book chapter on user tracking by my friend Philip Greenspun might be useful.