First, the basic facts: Cookies are not, and cannot become, executable programs, let alone self-executable ones. They are tiny text files, placed on a computer by a Web server and readable only by the server that placed them. Aside from basic anonymous information like browser type and IP address, cookies contain nothing that the user has not voluntarily supplied. They cannot be configured to do more - if they tried, the user's browser would reject them.
Cookies are, in fact, no more than the innocent lubricant without which the Web's machinery would come grinding to a halt. When you buy things online, a cookie is what makes your shopping basket function. When you return to the site to reorder the same things, a cookie is what tells the site which database record to access to call up details of your past orders. In fact, whenever you go online and experience any degree of personalized experience, a cookie is probably responsible. But, unless you have actively provided personal information to the site that placed the cookie on your computer, it can convey none.
The basic act of delivering a cookie to your computer and later accessing it never involves, and is intrinsically unable to involve, the gathering of any personally identifiable information about you. A tracking cookie can, indeed, be used to gather information about pages viewed on your computer (but only on sites with which that cookie is associated), and that information can be used to serve you ads or content that more closely match your interests - but the information gathered is completely anonymous and utterly untraceable to any individual.
In fact, if cookies were crippled, you could expect that users trying to navigate the Web would be assaulted by a succession of permission-demanding dialogues, probably in the form of pop-ups, as they did so. Their progress would be slowed to a near halt and many sites would be rendered effectively unusable. The Web in its current form might well collapse, as users would be unable to reach the content and advertisers would be unable to reach the audiences that they each wanted.
At its most basic, it comes to this: Should Web sites remain mostly free and continue to get better? Or should cookies be crippled and the entire commercial sector of the Web be put at risk? My answer is that not only are cookies incredibly useful, but that accepting them on one's computer is the negligible payment one makes for a free service (i.e. the Web) of enormous richness and variety.