My 2 satoshi's worth:
btc-e (pretty reliable for the most part, unknown people behind it a fairly large concern)
bitstamp (reliable, solid)
cryptsy (has it's issue(s), but best overall place I've found for my alt trades)
Coinarch has just released a Private Beta and is focused on security. Check out how we're dealing with security here -
https://privatebeta.coinarch.com/Info/Security.
Coinarch is not an exchange like the providers mentioned above. We are an online platform offering innovative trading solutions for Bitcoin. You can do more than just buy and sell bitcoins at Coinarch.
We are really excited about our Private Beta and would love to hear what you think. Register your interest at
www.coinarch.com and we will send you an invite code.