Apply Scale and Rotation in Blender 2.5

Does anyone know where the apply transformations function went in 2.5? Under the object menu I see clear, but where I would normally expect to see apply there isn’t anything. Any idea if its unimplemented at this point or if it is called something else now? Thanks!

P.S. I actually need to do it via script so if you have that code instead that would be great.