[kovidgoyal]

Bash is so last century Save the following as batch.py in the directory wth your epub files. Then run it as either

python batch.py
or
calibre-debug -e batch.py

#!/usr/bin/python
import os, time, glob, subprocess

files = glob.glob('*.epub')

workers = []
while files or workers:
    while len(workers) < 4 and files:
        f = files[0]
        files = files[1:]
        w = subprocess.Popen(['ebook-convert', f,
            os.path.splitext(f)[0]+'.mobi'])
        workers.append(w)
    for w in list(workers):
        if w.poll() is not None:
            workers.remove(w)
    time.sleep(0.1)

Change 4 to the number of worker processes you want.