Utility for Video Format Conversion

I am looking for someone to create a program using maybe some open source tools that is reliable and efficient in converting Video formats. The tool will have API or web services defined to provide the File Name, location and type of file ("avi", "wmv", "mpeg", "mp4", "h264", "mov", "flv", "3gp", ) formats as input and take the output format and convert it into the appropraite format. I am not looking for User Interface (but for testing it may be OK), I am primarily looking for a programming interface so that the process can be automated. It should be able to take any format and covert it into one of the above format as well as iphone format of the video. It should have the ability to encode at a fixed bit rate and resolution or even at a variable bit rate and defined resolution. The out put file location and file name will also be given during the request through the API or Web Services. All other suggestions are also welcome. Programming Language is fine, till the time it can be supported on Windows Server 2003 and Windows Server 2008 as wells as Windows 7.