With the global Pokemon fever of the nineties and its recent revival, you will invariably run into this cute little lightning fighter and his cohort. There are specialized Pokémon stores all over Japan, but you can always look for Pokémon merchandise in any department store.
Totoro has become the de facto mascot for Ghibli--a sort of bigger, fluffier Mickey Mouse that has been around since 1985. Totoro and his fellow Ghibli icons are prevalent throughout Japan. Of course, if you are keen on getting up close and personal with Totoro, be sure to visit the Ghibli Museum in Inokashira Park (Mitaka).
3) Son Goku (Dragonball)
One of the key things that pulls fans into the Dragonball world is its deep and diverse cast of characters, but at the forefront of it all is Son Goku, who can still be seen both in child and adult forms throughout Japan after over 23 years in existence. Dragonball goods are available in most department stores.
In fairness, Gundam is not a specific character, but the name for giant mobile suits used for interstellar battles. Gundam has been around since 1979 and has become entrenched in Japanese pop culture, appearing in themed restaurants, TV ads, videogames, and having a fifty foot statue standing outside of the Diver City mall in Odaiba (unfortunately, the Gundam statue was recently retired)--even Japanese politicians have adopted Gundam for promotions (see pic below). As a personal anecdote, when my daughter was born, I told my Japanese friends that we named her Matilda, and their collective first response was, "Oh, like Lt Matilda from Gundam!" Of course, that was not the reason we named her that, but it made me chuckle to think that would be the first thing that would come to mind for them.
5) Lupin III
Before Marvel had Daredevil, Japan had Lupin III, a wise-cracking, fourth-wall breaking anti-hero. Inspired by a French fiction writer, Lupin III was created as the grandson of fictional French thief, Arsène Lupin, and has adventures continuing his family's thieving ways, occasionally ending up an accidental hero all over the globe. Although he has reached fame internationally, at home, Lupin IIII remains an important staple for domestic manga and anime fans alike. In fact, Hayao Miyazaki (of "Totoro" and "Spirited Away" fame) cut his teeth on Lupin III, earning his directorial debut on a Lupin film called "The Castle of Cagliostro."
Well, that does it for Part I. Check out Part II!