brad,
I don't think you will be able to regain much strength by filling holes. Especially in a beam. If more strength is needed, your best bet is to get another bigger or sounder piece of wood. An engineer is a good person to have on your team if there is any doubt (and there usually is or at least should be).
Now, if you don't like the looks of the empty holes, then plug away. I personally would rather look at legacy joinery than contemporary dutchmen.
gook luck with your project,
Gabel
