Just add a tiff file with a name e-mail.tiff into the folder ~/Library/Images/People, restart Mail.app and you are done.
So for Flattr e-mails, you would have the logo at ~/Library/Images/People/no-reply@flattr.com.tiff.
There are more details contained in this blog post.
[crarko adds: I haven't tested this one, but it should work with most, if not all, versions of Mail.]

