Consider taking a look at CampBX.com if you're in the United States. They're a new exchange that has gone to a lot of trouble to prove to the community that security is a primary concern for them.

Another exchange that you didn't list is Bitcoin7.com. They're less well known than the two you listed, but they've risen to #3 in volume on several occasions and seem to be handling it fairly well.

As for fees, the majority of these exchanges are charging 0.3% right now, whether to compensate for the hack (Mt. Gox) or as part of a summer special (TradeHill). Typical fee rates are around 0.65%, at least that would be Mt. Gox's normal rate. As MikeCa said, look on their websites. They'll list the rate somewhere.

Dwolla charges a flat $0.25 for all transactions. Great if you're doing large amounts, not so great if you're looking to do a lot of small ones.