Let me give you one example and perhaps if you want to know more about specific software, you can post a more detailed question. There is a new add in for MS Project called Barbecana Full Monte. Full Monte is a Monte Carlo simulation. Essentially Full Monte simulates your project schedule thousands of times and examines the probability of successful outcomes -- so it focuses on scheduling risks. From the web site:
Barbecana specializes in risk analysis software for the project management industry. A passion for fast, elegant code results in some of the quickest, feature-rich risk analysis software available in the market. Barbecana’s risk software is perfect for those in aerospace and defense, construction project management, technology project management, engineering, government contracts and more.