There's a chain in Tokyo called Cheesecake Cafe. If you are craving dessert check it out.
This place is not comparable to say the Cheesecake Factory in the states but still, if you want something sweet...
They have a nice display case for their desserts that will make your mouth water although you will get the Japanese dessert experience which means the serving sizes are very small. Of course you can look at that as a good thing because you won't get as fat.
They also have regular meals if you want something to eat. Mostly pasta and sandwiches.
There are two in Shinjuku, one in the basement of Studio Alta across from the east exit of the station. Another is also on the east exit between the old Kinokuniya bookstore and the Isetan department store. There's also one in Daikanyama and one directly across from Shibuya Station, the Hachiko exit in the 1092 building.