I've been using most of the exchanges for the last six months. In order of reliability for me:

Reliable so far:
1) Coinbase
2) Bitstamp.net (Coinbase's exchange)
3) Cryptsy - only used to buy alts.

Usable and reliable so far:
1) Crypto-Trade
2) Kraken
3) CoinEx

Completely unreliable :

1) BTC-e - run by known scammers. Selectively target high value accounts. Have lost many BTC from them seizing my account for no good reason other than I created a second (verified) account. Support completely unresponsive.
2) MtGox - run by non-finance types who are fairly comical in their support. Nothing stolen by them but they will not give USD out so they are useless for fiat cash out (not important to me). Have used them to buy BTC but they are always the most expensive.