Earth Kitchen Company on Marutamachi offers Japanese “Obento” lunch-boxes that are completely natural, chemical-free and super-nutritious. They have a variety of lunch-boxes on offer; meat-based, fish-based and tofu-based and all are priced at ￥735. In addition to the tofu lunchboxes, vegetarians can also enjoy the veggie salad croquettes, soybean croquettes and deep fried gluten (麩) bentos. All of these come with rice and a variety of seasonal veggie side dishes. This is basically a take-away establishment, though there are a couple of seats available if you want to eat in the store. However, if the weather is nice, a picnic by the Kamogawa is highly recommended. Below are some pictures. Click through to flickr for a closer look.

Earth Kitchen also sells a variety of other eco-friendly foods and products. It can be found on the north side of Marutamachi Street, three doors east of Keihan Marutamachi Station, Exit #4.
Opening hours: 10:30 – 18:30 (Closes 17:30 on Thursdays and 15:30 on Saturdays).
Closed on Sundays and national holidays.
Tel/Fax: 075-771-1897
All lunches are hand-made on the premises so be sure to give advance notice if you are ordering for a large number or people.
Here is a map.