I need to project some dynamic layers to Web Mercator. The geometry service only projects geometries. Is there a geo-processing tool in ArcMap for this? Or any suggestions how i could do this without altering the map services.
With a dynamic map service, you can simply request it in a different coordinate system using the spatialreference parameter.
See this code sample which shows how you can define a custom extent and spatial reference, and then add a dynamic map service on top, and it will reproject it self to match the coordinate system. Note that there is a performance hit for doing the reprojection.