The normal way of associating a picture with an e-mail is using the Address Book. While this makes sense for the humans I'm interacting with, I don't want to add an address book entry for no-reply@flattr.com. You can get around this by using an old NeXTSTEP era mechanism that still works in Lion.
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.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20111110233800986