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What U.S. banks offer two-factor authentication (such as password & token) for online banking? 
Bank of America supports two-factor authentication using SMS messages, similar to PayPal. You can enable the feature from Online Banking under Customer Service -> SafePass Settings. Update: Over the weekend of July 28th, 2012, the SafePass control on the authentication page was updated to simple HTML + JavaScript instead of Flash, so that it is now possible to login from Safari on iOS, among others.