It's hard to tell if there are any other issues without an example file but it looks like you might have missed a few 'end' statements.

begin

  filedir = "/Volumes/LABDOCS/StudiesCurrent/FirstSteps/Studies/FS_MomResponse/OpenSHAPA/Export/"
  filenames = Dir.new(filedir).entries
  dir = File.expand_path("~/Desktop")
  out_file = File.new(dir + "/MomResponse_IdBidstatMomcodeMomtrans.txt", "a")

  for file in filenames
    if file.include?(".opf") and file[0].chr != '.'
      puts "LOADING DATABASE: " + filedir+file
      $db, proj = load_db(filedir+file)
      puts "SUCCESSFULLY LOADED"

      id = getVariable("id")
      bidstat = getVariable("bidstat")
      momcode = getVariable("momcode")
      momtrans = getVariable("momtrans")

      for idcell in id.cells
        for bidstatcell in bidstat.cells
          if bidstatcell.onset >= idcell.onset and bidstatcell.offset <= idcell.offset
            if bidstatcell.bidstattoemo != "n"
              for momcodecell in momcode.cells
                if momcodecell.onset <= bidstatcell.onset and bidstatcell.offset <= momcodecell.offset
                  for momtranscell in momtrans.cells
                    if momcodecell.onset == momtranscell.onset and momcodecell.offset == momtranscell.offset
                      out_file.syswrite(idcell.study + "\t" + idcell.id + "\t" + idcell.sess + "\t" + idcell.educ +
                          "\t" + idcell.tdate + "\t" + idcell.loctype + "\t" + idcell.sex + "\t" + idcell.raceb +
                          "\t" + idcell.racem + "\t" + idcell.ses + "\t" + idcell.mbdate + "\t" + idcell.bbdate +
                          "\t" + idcell.beldate + "\t" + idcell.hkdate + "\t" + idcell.wdate + "\t" + idcell.lang +
                          "\t" + idcell.crudate + "\t" + idcell.wdate2 + "\t" + idcell.mvocab + "\t" + idcell.maction +
                          "\t" + idcell.mgesture + "\t" + idcell.mactwobj + "\t" + idcell.mpretend +
                          "\t" + idcell.mimitate + "\t" + bidstatcell.ordinal.to_s + "\t" + "statbid" +
                          "\t" + momcodecell.ordinal.to_s + "\t" + momcodecell.objcode + "\t" + momcodecell.verbcode +
                          "\t" + momcodecell.actcode + "\t" + momcodecell.loc + "\t" + momtranscell.ordinal.to_s +
                          "\t" + momtranscell.verbal + "\t" + momtranscell.action + "\n")
                    end
                  end
                end
              end
            end
          end
        end
      end

    end
  end

end