I did it over MSN Messenger. (Back in the days when it wasn't Windows Live Messenger, good times.)
Just move your keyboard/or if you had desktop space, place your cards there.
Then just type to your opponent your actions. (Of course, most opponents want a clean, crisp understanding of what you're doing so they can imagine your side of the field better...
...However, if you're playing someone you know is a big a doofus as you are, then you must roleplay, in the most stupid and silly ways possible, and constantly make crack references to YGO the abridged, because that's how real people play children's card games!