Hi Nate,
We do this manually using Member Status updates in SFDC. Once a lead replies to an email, we change their Status in the Campaign.
If this is too tedious, and if you respond to each email reply, you can track replies by using Salesforce's "BCC to Salesfore Email." Since this BCC email logs a Completed SFDC Task, you can create a Marketo Trigger based on a Completed Task being logged, based on the Task's Subject line.
Would be interested to learn how others are managing replies.