The fact that Flash had it's own cookies that weren't cleared by private browsing modes was a big story (don't know if they've fixed that yet) but there's a general problem of Zombie Cookies (as long as one ID method works the others can be recreated) and Panopticlick (ID you uniquely based solely on the random info, like installed fonts, sent to the server by your browser).

http://en.wikipedia.org/wiki/Zombie_cookie

https://panopticlick.eff.org/