I don't think there is a way to filter based on size of attachment (I would like that myself).
For the emails sent from BES or redirector, this isn't really an issue because there presumably isn't a size limit on your Outlook mail that matters here. As Jibi says, the entire attachment would not be downloaded to the BB unless you explicitly asked for it, so wireless usage will not be affected either.
For BWC, the best you can do is recognize when a large email has been sent to you, and then delete it on the BB. If you have set up your blackberry to synchronize with the BWC inbox, then it will be deleted there and not overflow your space allocation.