You can't change a browser's homepage - In all browsers I know, it asks you if you want to change your homepage ( I believe ). Javascript has been used for so long and so widely that I don't think there are many (if any) security problems that remain.

With regards to ebay - That problem is not a javascript problem as far as I'm aware, but probably a problem with activex controls or the like. Javascript can't "install" anything on your system. It can probably log keypresses...but only for the page you're on.