This code use the Blender Python API to batch convert 3D model file with ''ply'' format to ''obj'' format. It is only tested on Blender 2.64.

ply2obj.py

import os
import bpy

# put the location to the folder where the plys are located here in this fashion
path_to_obj_dir = os.path.join('D:\\', 'Workspace\\Data\\scapecomp')

# get list of all files in directory
file_list = sorted(os.listdir(path_to_obj_dir))

# get a list of files ending in 'ply'
ply_list = [item for item in file_list if item[-3:] == 'ply']

# loop through the strings in ply_list and add the files to the scene
for item in ply_list:
    # full path and file name
    path_to_file = os.path.join(path_to_obj_dir, item)
    # import ply into the scene
    bpy.ops.import_mesh.ply(filepath = path_to_file)
    # change suffix to ".obj"
    portion = os.path.splitext(item)
    newname = portion[0]+".obj"
    # new full path and file name
    path_to_file2 = os.path.join(path_to_obj_dir, newname)
    # export current scene to an obj file
    bpy.ops.export_scene.obj(filepath = path_to_file2)
    # delete the object from the scene
    bpy.ops.object.delete()