They're all separate entities with their own rates of exchange between BTC and other currencies. When Mt. Gox first suspended USD withdrawals, their price diverged pretty quickly from the other exchanges.
Scarsbergholden is referring to the withdrawal of crypto currencies, which is what Bitcoin is. Mt. Gox and CampBX, for example, allow you to send/withdraw BTC for no fee, but charge fees for buying and selling. BTC-E charges a fee for Bitcoin withdrawal.
Understood. Overall, as of right now, is it a wash? I could be misunderstanding the fees, Gox seems a bit higher. No pun intended.

Yeah, it's pretty much a wash. Part of the decision should be based on the volume you plan to trade in: if you have hundreds of Bitcoins you want to actively trade, you're best off on Mt. Gox because they have the highest volume by a substantial margin. If you're planning to trade, say, 5-20 BTCs, you could trade on any of the exchanges without having to worry about your orders causing big price swings.
Any thoughts on using a separate wallet?
It's always a good idea to use a separate wallet for any BTC you're not planning to actively trade. A properly-secured local wallet is substantially more reliable than any exchange, since the exchange could go offline at any time with no warning. Unlike bank deposits, your funds on a Bitcoin exchange aren't insured in any way, so if the exchange disappears, there's a good chance your money's just gone.