The old Radio Kaikan building was an Akihabara landmark. It was the first stop for many anime fans and was even featured in a video game. In late 2011, it closed down after nearly 60 years of service - a structure that was certainly dated in design and earthquake strength. Photos of the building before its closure show cracks in the walls from previous earthquakes. After almost three years, the new building reopened to much fanfare. The line was literally around the block on opening day just to see what was inside.
While most of the original tenants moved to one of three buildings on a temporary basis, a few probably relocated for good. And with more space now, there are additional stores inside than before. The marquee stop is probably the Ginza Lion restaurant on the first basement floor. I've been to a Ginza Lion restaurant before and the food is decent and not too expensive.
There's a convenience store on the first floor, now the most convenient to those coming out of Akihabara Station. The window/walls have an advertisement for the highly popular Girls und Panzer series, and the chain has a couple anime cardboard cutouts out front.
There's also a well-stocked Akihabara gift shop, though there isn't anything truly unique here. Many of the items here can be found in Don Quixote; I haven't done enough checking to see if this is a new gift shop or if it relocated. There's also a card gaming store just inside the building entrance.
Moving to the second floor, you get into real geek territory. These display cases are rented out by individual collectors to sell extra or unwanted figurines, so each box can have something unique, and the stock changes out pretty fast. Prices are hit-and-miss in stores like this, and you should definitely shop around.
One wall has a bank of vending machine toys. Gachapon toys can be quite limited, and many of the ones found in Akihabara might not be easy to find elsewhere.
There's another large CCG shop.
And an actual electronics store. Stores in Akihabara generally focus on one specific aspect, and I believe this store's specialty is video surveillance.
Moving on up, the third and fourth floors belong to K-Books. I haven't spent much time in K-Books, though they have books, CDs, DVDs, and some anime figurines.
The fifth floor has several small shops selling various anime and manga goods, plus another electronic components shop. I also saw a K-Pop/J-Pop shop with posters and other flat goods.
Yellow Submarine is up on the sixth floor, and is my favorite store in the building. It has a very large CCG card collection, but I come here for the baseball cards. The store covers the entire floor, and also includes models as well as large and small figurines.
There's a doll shop on the seventh floor with very expensive dolls.
You'll also find pop culture goods here mixed in with more anime and manga merchandise.
Another CCG shop is on the eighth floor.
You can also find more models and dolls on the eighth floor.
Phantom, a military goods store, is on the ninth floor. It shares the space with a limited-time merchandising event store (that's hard to explain) as well as a Radio Kaikan store that had an interesting collection of goods and Radio Kaikan souvenirs (t-shirts, etc). The top floor is event space.
Akihabara should be explored, of course. The sights found on the back streets and along Chuo Dori are worth seeing, and there are several other stores to browse. But this is arguably the best place to shop in town for anime and manga goods.
Access is pretty easy from Akihabara Station. Just take the Electric Town exit and turn left out of the ticket gates; follow the road to the right and it's the second building on the left. You can see it as soon as you exit the station (see my first photo). The stores are open 10:00-20:00 (sometimes less); the Ginza Lion restaurant is open 11:30-20:00