The main two I use are cryptsy and coindup, coinedup has much lower volumes but is a good site that responds well to your inputs while having a decent selection of altcoins. Cryptsy on the other hand has a pretty GUI with large volumes and a lot of coins BUT (and that's a big but) it can be incredibly slow and just generally buggy.

With Cryptsy you have to watch for things like if you complete a trade you can be credited with the bought coins long before the sold coins are processed, if you then sell the coins again (by mistake) you will be left with a negative account which blocks withdrawals and if your unlucky and the exchange rate drops it can leave you in debt... if that happens don't count on support to help. Everything goes through eventually so I would just warn you to keep track of what you're doing and don't just rely on the numbers you see on the site, and don't count on things happening fast, sometimes they will but sometimes it can take 1/2hr+ just to return your coins to your account from a cancelled order. The learning curve on that site can be very frustrating and if another site had the same variety of coins and volume of sales while being fast and reliable I'm pretty sure Cryptsy would just disappear but alas atm there is no other equivalent (that I know of anyway).

I mainly use Cryptsy for trading because of the volume and variety so it is usable but just be cautious.

The others I know of but don't use much are;
MtGox
BTC-E
Vircurex
Coins-e
Bter
VirWox - You can get money to BTC on this by buying 2nd life money with paypal then trading to BTC, it can be handy but if you don't have an established account the withdrawal can take a couple of days to process, fees can be steep too but its the only way I know of to go paypal->BTC with relative ease.