Can you use Python? You could use some for cycle. I tried to write some concept here:
import os
wd = r"c:\your\working\dir"
os.chdir = wd
list_of_files = os.listdir(wd)
file_that_clips = "path_to_shapefile_that_clips_other"
for file in list_of_files:
if file[file_to_clip[-3:] == "shp": # If file is a shapefile
clipped_file = file[file_to_clip[:-4] + "_clipped.shp" # New name for output
os.system("ogr2ogr -fclipsrclayer ESRI" Shapefile+ file_that_clips + " " + clipped_file + " " + filefile_to_clip) # Execute cmd order
I'm not sure about the ogr2ogr Clip statement. But you could copy there yours.