BTC-E has been seen by the Bitcoin community as "shady" for years. People have always recommend others to avoid using it. It was rumored to be an easy place to sell stolen Bitcoins. It has always offered strangely convoluted pathways to transfer fiat to financial institutions (see http://bitcoinworldwide.net/how-to-deposit-money-into-btc-e). I'm glad BTC-E finally got taken down. I am not surprised it was involved in illegal activities. One less shady Bitcoin company.

Now the top 12 or so volume-ranked Bitcoin exchanges listed at https://cryptowat.ch are perfectly legitimate trustworthy companies. The ones I'm not sure about are CEX.IO and Luno (not saying they aren't trustworthy, I just don't know them that well) and, well, Bitsquare which as a decentralized exchange is bound to have some shady participants.