Budget
Shakey's Pizza
Shakey's Pizza has an all-you-can-eat lunch buffet for ¥850 on weekdays on weekends & holidays about ¥1250. If you've never had seaweed, pickled ginger or fruit salad in your pizza, this is the place to try it. The pizza isn't great, but for Tokyo the buffet is a killer deal.
Arms Sandwiches
This small, Americana-inspired eatery is nestled right off the main footpath, and serves lots of Western food, including a wide burger selection try the avocado burger!. Also serves fries, chili dogs, and other non-Japanese fare. American beer selection available. Be advised, the place fills up pretty fast, so swing by before a stroll in Yoyogi and put your name in it.
Midrange
Omote-sando has occasionally been dubbed the Champs-Elysées of Tokyo, which is true at least for the general price level of the trendy cafes and eateries along the road.
The must-eat item of Takeshita-dori is the Harajuku crêpe. It's a treat of a fresh-made crêpe rolled into a cone and stuffed mostly with whipped cream and other goodies such as strawberries, chocolate, even whole slices of cheesecake; the more adventurous options including tandori chicken. Just stroll down the street and you will see four or five different shops. Most flavors cost less than ¥500.
In terms of eating a meal in Harajuku, the vast majority of restaurants serve Western or Indian food. If it's Japanese food you're looking for, you're probably best off eating before or after Harajuku.
Fonda de la Madrugada
Located in a cavernous basement, Fonda de la Madrugada is regarded as one of the best Mexican restaurants in Tokyo. Menu in English, Spanish and Japanese.