A survey in 2009 found that more than 50% of websites were using Flash based cookies to store data.Most people were only aware of regular browser cookies that they removed, thinking that websites could no longer track them.
Each web browser stores regular browser cookies in its own location. None of the browsers look for cookies in the locations that other browsers store them in. But websites started storing information in Flash based cookies called Local Shared Objects(LSO). These cookies were stored in a location accessible by all web browsers.
When a user deleted their regular browser cookie and then visited a website, the website would simply read the LSO and repopulate their regular browser cookie. Unless users knew where the LSOs were stored, they could not prevent websites from tracking them. There were tools like BetterPrivacy (FireFox plugin) and CCleaner that could clear LSOs, but not many people were aware of them.
Now, Adobe has worked with Mozilla and Google to come up with an API that can be used by FireFox and Chrome to delete the LSOs without the use of 3rd party plugins. Removing LSOs can be an option when you delete your browsing history in the web browser.
Not sure if IE and other browsers will also support them. But since the LSOs are accessible by all web browsers from a single location, deleting it from FireFox or Chrome will make them unavailable for any other browser.