I've noticed that for the Opera browser, CCleaner misses a couple of folders. This is the \images folder which contains favicon.ico from visited sites and \vps which according to one forum poster contain autocompletion information, but can grow to surprisingly large sizes. In addition, I don't know if Ccleaner touches the vlink4 which lists visited files.
Also note that for the upcoming Opera version 10, which I've tried the beta of, the folder locations are re-arranged somewhat.