It seems like I've neglected to talk about my new favorite tea shop - a Taiwanese tapioca milk tea place called Chun Shui Tang 春水堂 that has come to Japan. I don't actually like tapioca that much (I'll eat it without problems but I don't need it) but I love milk tea that has a strong tea flavor - Chun Shui Tang does that nicely! The nicely-furnished shops in Omotesando, Daikanyama, and Roppongi Icchome all have free wi-fi too, which is a nice bonus.
Also, Ginza Budou no Ki 銀座ぶどうの木, a French-style "Maison de Dessert" Japanese dessert parlor, has my favorite chocolat fondant in Tokyo so far. The accent of pepper is amazing. Their Crepes Suzette and Cheese Souffle are famous too, I believe.