Since I know many others have similar moral (or health) concerns, I started listing some of my favourite haunts across the city, where you can get cruelty free tastiness!
Lets start in Roppongi, of all places. A short stroll from Mori Tower you will find Chien Fu (which also has a sister restaurant in Kunitachi). They specialize in Taiwanese style vegan food, with the fake meat the country is so famous for. The sweet and sour 'pork' is a major favorite, and their huge teishoku sets are all around 900yen. You can buy bags and cans of fake meat, vegan ramen and tofu mayonnaise on your way out too!
Next up is Kagetsu, a major ramen chain. During the spring they have vegan ramen, gyoza and fried rice. Cheap and cheerful.
(NB. This is the last year they will be serving it, although you can buy the gyoza and ramen from their online store!)
(I ❤ gyoza, can you tell?)
A hidden gem, if you so happen to be between Azabujuban and Shirokanedai station, is King Falafel. This used to be a twice monthly treat, when I worked in the area. The owner is lovely, and the full sized sandwich is a serious meal, with freshly fried falafel. Serious yum, but only two little chairs outside for seating.
On the same lines, Shamaim near Nerima is a bit of a hike from central Tokyo (unless you live there, of course), but has a fabulous falafel set and hummus set.
For something with a more American flavor, Good Honest Grub (housed in what appears to have been a normal house, between Shibuya and Ebisu) has an excellent Mexican bean wrap and smoothies.
I have already written extensively about Eat More Greens (near Azabujuban Station) here, where the menu changes with the seasons (and has the most amazing Valhrona chocolate vegan doughnuts).The same goes for Deva Deva in Kichijoji (info here).
There are several more places I wish to go, and there are definitely some that have slipped my mind at the moment. I really want to check out T's ramen (inside Tokyo station) as well as the larger T's Kitchen in Jiyugaoka.
Any recommendations? I would love to hear from other veggies in Tokyo!