If you're a control freak you'll love WordPress.org.
You have total control over your website when you use WordPress.org over WordPress.com
How would you like to be told what you can and cannot have on your website?
If you're an affiliate, don't even think about using WordPress.com as they will not allow you to use any affiliate/referral links on your own website.
If you're monetizing your blog with ads, don't even think about using WordPress.com as they will not allow you to use ads such as TextLinkAds, Adsense, Yahoo and others.
This is very interesting to me because they may include ads on your blog although you do have the ability to turn them off.
Did you know you cannot have a custom theme on a WordPress.com hosted site? That's right you can "customize" their free themes, however you cannot really personalize the themes. You also cannot manipulate the PHP code behind the scenes.
This may not matter to you however when you need a certain item added to your site, your web designer or developer may be limited because of WordPress.com restrictions. There are thousands of plugins and millions of downloads and widgets that can be used on WordPress.org, however these cannot be used on WordPress.com.
I know it's really confusing, however the most important thing is if you want total control of your website and/or blog go with WordPress.org.