I think what your trying to describe is an XSS ( Cross Server Scripting ) attack that steals your cookies. I'm not sure how "your passwords all kept in browser are leaked"... that's just not possible on any modern browser I am aware of.
This XSS attack is possible if there was a bug in btc-e's site that allowed for code to be injected into the page through a GET request, but probably not the case as many of us who's accounts were hacked never clicked any links in the "trollbox". As far as botnets and virus and java exploits, many of us also run linux which is the most secure desktop available and also chrome which does not allow java to be ran without a confirmation first!
java zero day. Chrome://Plugins then disable any Java plug-ins. this is different than javascript. Linux is not immune.
has anybody tested if you can create API key, then withdraw with it? probably no email confirmation.