I'm surprised this chain is not already on here. Alice in Magical Land, the Shinjuku West outpost of the chain, is a lot of fun. If you like cute food and themed restaurants, this is a great place to come! Unfortunately it's really expensive, there is a 500 yen cover charge (two hour maximum) and they automatically add 10% tip (a bit unusual since there is no tipping in Japan). The food is all fairly reasonably priced, but the portions are haute cuisine style - super tiny. My friend and I split three food items and each got a dessert and a non-alcoholic drink, and the total was nearly 6000 yen.
You're paying for the atmosphere too, of course, and that was a lot of fun. I loved the Cheshire Cat Berry Parfait, which was vaguely shaped like the cat himself, and even had chocolate sauce paw prints on the dish. The decor is fanciful and the waitresses even dress like Alice - although their skirt is half the length of hers. (I asked my Japanese friend about this - apparently the young women who work as waitresses at this type of place would find a knee-length skirt like Alice's too frumpy.)
I had a great deal of fun here, to be honest. Yes, it's expensive, but I thought it was worth it, and the menu was easy to understand because every item was marked in English. The only thing that wasn't in English was the description of the contents of the special house cocktails - so you could order the White Rabbit Cocktail, for example, but you wouldn't know what was in it. Other than that, everything was in English.
Definitely worth a trip if you're into this kind of thing!