Unless you are desperate for one of these deals, don't go to Toys R Us on Black Friday. (or Thanksgiving itself, for that matter) I've been there. And I can confirm that I had to wait in line for almost 5 hours just to buy a small smattering of games. Thankfully, the games I was there for did not seem to be hotly contested. Most of the shoppers there were far more interested in the numerous other deals. So there were plenty of copies available when I got up to the register. I didn't have to face down anyone over who got the last copy of anything, and thank goodness. Some of the mothers I was standing in line with were not to be trifled with. I do not think I could have stood my ground against any of them.
Toys R Us is ground zero for Black Friday. They are much more organized than stores like Wal-Mart or Target. But EVERYONE shows up to Toys R Us. The demand for all those children's toys for Christmas shopping is insane. And while the demand for individual video games doesn't tend to be as high, the games are kept in the electronics section. And the electronics section is also home to all of the door-buster sale tablets. And the demand on those seems to be crazy high. Everyone is buying tablets for their kids these days. So the line for the electronics section won't be any shorter, even if the items you're shooting for aren't in high demand.
For Black Friday, your best bet is to go to Wal-Mart first, but don't line up early. In fact, you're better off not being there when the store opens. Just head to one a half hour after it opens. That will minimize the risk of you getting trampled. (or any other type of physical confrontation) Most of the individual game deals will still be around for a few hours after the doors open. Some of them will endure for most of Black Friday.
You should line up for specialty stores like GameStop. Those stores are smaller, and can't afford to buy in as much bulk. So a lot of their supply is going to be more limited. They are also a lot more targeted in their commercial focus. Anyone who goes there is going to be directly competing with you for game sales. A lot of the consumers at Target and Wal-Mart will be shopping for non-gaming deals, reducing the competition.