I do think that I would break things up into lots to drive up prices. I don't know how big the lots would be. More than likely, the rare/valuable games would be sold separately and the commons in 10-20 game lots, some with systems.
Thats probably the best way to do it. The common games usually never sell for high prices anyway, and bundling them with consoles will help to get rid of them.
And of course, those rarer ones will do just fine by themselves.