Meats

Beef - Gyuniku

Chicken - Toriniku

Eggs - Tamago
Eggs are often served simply boiled or made into omletes. In Japan, people often put sugar into their eggs before cooking to make sweet omletes. Eggs are also eaten raw in some food dishes. Chicken and quail eggs are used.

Pork - Butaniku

Sausages (cut into octopus shapes!)
Mini-sausages are used in bento. What tickles me is that sometimes they are carved into octopus shapes which looks adorable.
I bought some mini-sausages from a Japanese food store one time and went home and cut slits down on half of them to make 6 legs (if I made 8 they would be too thin and wouldn't be as sturdy). I wanted to heat them, so placed them in lightly boiling water. Much to my surprise (and delight) the cut slits curled outward upon hitting the water. The octopuses (octopi?) looked perfect!

Proteins

Red Beans - Azuki
Azuki beans are used for sweet desserts in Japan as fillings in sweet breads or jellies. Azuki beans can also be mixed with rice.

Soy Products

- Green Soy Beans - Edamame
Edamame is a young soybean, picked and eaten out of the pod. Edamame is sold in the pod, or shelled. The shells are often salted as a snack, but only the beans inside are eaten.

- Miso
Miso paste is a seasoning made from fermented soy, salt, and wheat. Miso is often use to flavor broths or to simply make miso soup.

- Soy Beans - Daizu
Daizu are dried soy beans.

- Tofu