There are a number of tools for test management, some are targeted just to Waterfall, some are targeted to Agile, and some were built with the flexibility to handle any software methodology. Take a look at Software Planner (http://www.SoftwarePlanner.com), it falls into the latter category. It can manage more than just test cases (it can manage requirements, project plans, test cases, and defects), but it does have a rock solid test case management engine. The test case management area allows you to create a test library and test sets for test runs and it integrates with the defect tracking module. It has good traceability features that allow you to track all test cases and defects by requirement.
It also supports automated test case management (support for HP Quick Test Pro, Automated QA Test Complete, Rational Robot, Rational Functional Tester, Silk, etc). You can find a free trial from their website.
Hope this helps.