Is there absolutely no full header information for these emails? I can't figure where they would be coming from if they are completely in all respects blank. I guess the best you could do is filter them out with Rules. I can't be 100% certain this would work since I don't have a completely blank email to test it on, but you could do a rule something like this...
(make sure the last field in each condition category is empty)
If [all] of the following conditions are met:
[From][Is equal to][]
[To][Is equal to][]
[Subject][Is equal to][]
[Message Content][Is equal to][]
Perform the following actions:
[Delete Message]
(or to be safe have it move the messages to a folder until you know it works 100% by doing something like...)
[Move Message] to mailbox: [blank messages]
I would think something like that would work pretty well.
EDIT: Oh to do this I am assuming you are using Mail.app, if you aren't then just disregard this.