Well Bittrex is currently the top exchange by volume followed by Cryptsy. I like Bittrex a lot but I don't think it's design is as efficient as it could be.
I trade on 4 of the top exchanges (except Bter which I don't know very well). Mintpal is my favorite. It's got the cleanest design. I love the simplicity and efficiency.
I traded on Cryptsy for a long time, it was my first altcoin exchange. It's good but was very laggy at one time. Still it's one of the most reliable. Polo is ok (nice troll box
) but has the worst design of the lot.
Atm, I'm mostly on Bittrex for 2 main reasons, volume and the fact that they tend to add new coins faster than the others which is great for day-trading
EDIT - When I say top exchanges, I'm referring to altcoin exchanges not exchanges that focus on BTC-USD.
EDIT2 - For BTC-USD my favorite by far is Bitstamp