Looks like really helpful tool from SQL Query Optimization team at Microsoft.
Auto-indexing solution based on Missing Index DMVs - now works in recomendation mode but can be easily transformed to a fully automated tool. It also knows to clean up the mess - not only to create missing indexes but also to drop unnecessary ones. Though I wouldn't recommend to execute it in fully automated mode - at least not for dropping indexes. Take the tool's recommendations and check them first.
Another promising tool:
Visual Studio Team Edition for Database Professionals is due to be released at June 9th. Visual Studio + Team System + DB source control and, listen carefully, schema control - all in one tool. Hopefully also integrated together.