The Tokyo Game Show will be open to the public on the 11th and 12th. If you want to go on the first two days you'll have to trick them into thinking you're someone on the guest list, and then run like hell when the real guy on the list shows up. The show is in Chiba. Make sure you leave enough time to get there. The trains will be busy.
There is so much to do in both Tokyo and Osaka that you will never come close to doing it all, so just accept that up front.
If you want to have some fun learn Osakaben and see what kind of reaction you get from people in Tokyo and Osaka.
Thanks to the Densha Otoko dorama Akiba isn't what it used to be. It's still a good place to buy H Games, hugging pillows and stuff like that, but doesn't have the complete aniota factor of yesteryear. It's probably the best place on the planet for galge though.
Super Potato is probably the biggest game store anywhere. It also makes Japan-based eGay price gougers look reasonable. If it exists, Super Potato has it. If Super Potato has it, you can add an extra zero for the convenience. Try robbing them with a Metal Slug.
Cosplay cafes are always fun. They tend to cosplay new anime and games, so you probably won't see anyone dressed up as a Neo Geo character. Go to Akiba, find the nerdiest looking guy and offer to buy him a drink if he'll guide you to one. They're hidden in crazy hard to find places.
Speaking of nerds in Akiba, they all have money because they shop in Akiba. This is where you will go to rob people when you run out of money.
Should you be rich enough to go to Super Potato, you're also probably rich enough to spend a few nights in a cabaret. Bunny girls are hot.
Japanese pro wrestling is something you want to see live if you're a fan. Take a look at the sites in the puroresufan.com network for tour schedules closer to the departure date to see who is running where. HUSTLE is highly recommended if they happen to be running. Check them out at hustlehustle.com.
While you're in Osaka you might have a chance to see Osaka Pro. They have a cult following, although it's really Mexican in it's style. You either like it or you don't.
Den Den Osaka is everything Akiba used to be. Bring money. Lots of money. And then rob stores at metal slug-point because you won't have enough money.
Find a pachinko parlor in either city and lose some money. It's a great time.
If you haven't noticed a trend, everything is expensive in Japan. Whatever you were planning on bringing with you to spend, add a zero to that. I'm completely serious.
For general tourist attractions in Tokyo I'd recommend the Tokyo National Museum and Ueno park. In Osaka Exploland, Osaka Aquarium Kaiyukan, Nakanoshima Park and especially Osaka Castle are all worth your time. If you're an HG fan take a trip to Doyama-cho to see where he developed his gimmick. I wouldn't recommend bending over and yelling bachikoi unless you mean it though. Universal Studios Japan is in Osaka too if you're into that.
That should keep you busy for a week, but if not there's plenty more where that came from.