If BTC-E will have problems, then it will also hit hard on LTC price, since it's the biggest market for LTC.
I converted my LTC to BTC and transfered to stamp. I have always been nervous on keeping money in BTC-E, because their lack of transparency. They have a great interface and engine, but sadly I don't trust people that I know very little of. So, their confidence that everything will be fine won't make me very confident. Suffered a small loss because of this move, but I think that it was necessary to avoid the risk. I'm afraid that LTC price will drop more and there will be a lot of FUD, before it's known if BTC-E is in fact in trouble.
Lack of transparency is kind of an invalid point, given that the creator of Bitcoin is just as anonymous as the owners of BTC-E...
When the bitcoin software is open sourced, then the work itself is transparent and the exact person behind it isn't as important. But with BTC-E, their work is as hidden as their personal information.
Because of that I can't speculate if they did some shady deals with the criminal underworld or not. If russians can link BTC-E finance to terrorism, then the problem will go to international level and BTC-E will be in trouble.
I know that all of this can just be FUD without any solid base, but I had no reason to take the risk.
That is a very good point, if they can link it to finance terrorism then US, UK and the rest of the western world will move in, too.