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Cookienator (free) scans your PC for tracking cookies in multiple browsers as well as in Adobe Flash, and selectively deletes them while leaving the rest alone.
The small, simple program hunts for cookies from well-known sites such as Google, AOL and Yahoo. On startup Cookienator will report how many tracking cookies it found in various programs, including Internet Explorer, Safari, Firefox and Google Chrome (you may need to close all browsers before it will find cookies for each program).
While plenty of apps will clear out browser cookies, Cookienator goes a step further and also clears so-called Flash cookies. Though technically not cookies, the small files can be used for the same sort of tracking, and aren't deleted when you tell your browser to get rid of cookies.
You can check a list of all the to-be-removed cookies before clicking the Clean Now button, but you can't tell Cookienator to skip some and remove others. With a little manual effort, you can change the list of cookies it looks for by adding or removing new search strings used when scanning for cookies, such as *.youtube.com or *.advertising.com. The app's options also allow for only checking some browsers and leaving others alone.
If you don't use another method for clearing out tracking cookies, Cookienator is a simple solution. The BetterPrivacy add-on for Firefox is another good option for dealing with Flash cookies.