running several system commands in parallel in Python

If you are calling subprocesses anyway, I don’t see the need to use a thread pool. A basic implementation using the subprocess module would be

import subprocess
import os
import time

files = <list of file names>
command = "/bin/touch"
processes = set()
max_processes = 5

for name in files:
    processes.add(subprocess.Popen([command, name]))
    if len(processes) >= max_processes:
        os.wait()
        processes.difference_update([
            p for p in processes if p.poll() is not None])

On Windows, os.wait() is not available (nor any other method of waiting for any child process to terminate). You can work around this by polling in certain intervals:

for name in files:
    processes.add(subprocess.Popen([command, name]))
    while len(processes) >= max_processes:
        time.sleep(.1)
        processes.difference_update([
            p for p in processes if p.poll() is not None])

The time to sleep for depends on the expected execution time of the subprocesses.