I trade on the BTC-E is more than two years and have never, NEVER had any problems.
Problems has only noobs who open links in chat and after that hackers break their accounts.
I have also used BTC-E for a very long time, and never had any btc or altcoins lost, however, just like you silverston, the fact that we did not have a problem does not mean that anyone else do not have problems.
I do not click on any links in the trollbox, and to be honest, I think all links there should be banned altogether.
Accounts being hacked could be a simple case of beginners clicking malicious links, and then getting their accounts emptied, but we cannot also discount the fact that BTC-E might act in a way where they sometimes confiscate funds at will, or refuse to help random users.
A way to run an exchange could be to scam only a selective number of users, but not to such a large degree that users stop to use the exchange. This however would be quite unethical, but then again, some people are unethical. I'm not saying BTC-E is, but they're fairly known for providing extremely poor customer service.
The way I looked at is is that every time I send anything there, I mentally write it down as a possible loss, meaning that anything I send there I must be able to afford to lose.
Now - for accusations of scamming, it's necessary to collect as much evidence as possible, so make screenshots of transaction history, trading history, account details, account balance and everything else that matters, also note down all txid's, bitcoin addresses, and time lines of events. When presenting a case of fraud, be prepared to show all evidence that will not compromise your privacy.
Bitcoin foundation, Coinlab etc. will not help you with BTC-E problems, if they receive a large amount of complaints against btc-e with hard evidence, they might put up a warning against using the service, or being careful with it, that's as far as they will go.
This is an unregulated market, and then we as users must realize this.
I'm very sorry for anybody being scammed, but please prevent hard evidence when you bring forward scam accusations.