emaildata is a python package for extracting content from email messages.
From the examples:
import email
from emaildata.text import Text
message = email.message_from_file(open('message.eml'))
text = Text.text(message)
This combided with the standard python glob.glob()
or os.walk()
functions should make this a breeze to perform this as a batch operation.
- Gratis Yes
- Cross Platform (inc Linux)
- Batch/Script Yes
Testing it out
As an example, I exported an email from Quora, (Using Mozilla Thunderbird), as a file and fired up iPython:

Looking through it there were no =3D, =20 entries, (other than in a couple of the urls), but there were a number of sequences like \xe2\x80\x9cused car salesman\xe2\x80\x9d
that needed sorting out, these are unicode sequence.
Running: unicode(text, 'utf-8')
to decode and printing, (with a unicode compatible font), gives:

Where we find that \xe2\x80\x9cused car salesman\xe2\x80\x9d
is “used car salesman” note the up & down quotes.
If you need to decode the parts of a URL with query then you can use urllib.unquote()
to deal with them but for your usage you are probably not interested in URLs be they queries or not.