How do you manage the risks on Agile projects?

Prioritize them, same as in waterfall, but the application is a little different. Agile uses product backlogs to manage and prioritize features/stories and adjusts them to reflect not only value, but risk. That's why it's called a risk-adjusted backlog when that occurs. We do the highest value, highest risk items first wherever possible.

Jesus - On agile projects, you manage risk as you go by creating a Risk Adjusted Product Backlog, Risk Register and monitoring the same using a Risk Burndown Graph. Refer to Mike Griffith’s book, it is very well explained there with detailed example.

Jesus: Prior to the adoption of tools, choosing the appropriate agile method is far more important. For example, if the initial risk analysis shows that the requirements are not fully understood then, scrum would work. However, if the approach is clear and the team has worked together on a similar project successfully before then, CAS would a better approach/method to use. Many tools are common among different agile methods while there are few that help implement a specific agile method.