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Rice
Rice is virtually indispensable to any meal.  Gohan, or 'rice,' also is used to mean 'food' or 'meal.'  Steamed white rice is most commonly used, but fried rice and noodles also are used.
Onigiri
Onigiri, translated as 'rice balls,' are usually triangular, disc-shaped, or capsule-shaped.  Ingredients often are mixed in with the rice or stuffed into the middle.  There are many types of molds available to turn onigiri into bears, bunnies, and other whimsical shapes.  Onigiri is meant to be eaten with the hands and often has a strip of nori wrapped around it to keep the fingers from getting sticky.
Noodles
Many varieties are used, such as soba, somen, or udon.  Often yakisoba is included in bento, which is soba noodles stir-fried with various ingredients.
Egg
One of the most common bento ingredients, egg is served in various ways, such as tamagoyaki (a slightly sweet layered omelet), hard-boiled, fried, and scrambled with various ingredients.
Sausages / hotdogs
Sausages, or mini wieners, often are cut into various shapes using a sharp knife or molds to resemble animals and other objects, such as an octopus, a crab, or a flower.
Grilled fish
Salted salmon is a favorite.  I like to use leftovers from dinner - usually salmon, catfish, or trout.
Fish cake
There are different forms, including chikuwa (a tube-like form) and kamaboko (usually served in slices). 
Yakitori
Miniature kebabs are the cutest!  Traditionally made with chicken and scallions, you can use whatever suits your fancy.
Teriyaki-flavored meat
Chicken and beef are most popular, but you can use teriyaki sauce on vegetables, tofu, and even noodles, and it will taste great.
Yakiniku
Meatballs are delicious and oh-so-cute in bento.  Skewer them, serve them on pasta, tuck them into mini-sandwiches...the possibilities are endless!
Sushi
There are so many varieties out there.  I would advise against using raw fish, since most bento is not refrigerated before it is eaten.  I like using smoked salmon, vegetables, tofu, cooked meats, grilled eel, SPAM, shrimp, and other ingredients as filling.
Curry
Or kare, is usually served with rice.  A classic comfort food, Japanese curry is more mild and sweeter than its Indian counterparts. Curry is fairly liquidy and requires a watertight seal when packing in a bento.  I've found that Glad Press n' Seal works well to create a seal in 'designer boxes' that aren't meant for soupy items.
Chicken nuggets
Another fun and flexible food that is easy to prepare.
Dumplings
Gyoza, steamed buns, wontons, and other types of dumplings make for tasty bento fare. 
Croquettes
Or korokke, these are ingredients (e.g., beef and onion) mixed with mashed potato that are rolled in panko before being fried to golden goodness.  Once I figure out how to fry these properly, I will include them in my bento more regularly.
Tofu
Tofu puffs are healthy and easy to incorporate into stirfries, curries, and soups and are great eaten on their own (or with a bit of your favorite sauce). They freeze well too.
Cheese
Supermarkets sell bento-perfect cubes of cheese.  I also like the Laughing Cow wedges and the mini-Babybel cheeses.
Vegetables
Raw, steamed, simmered, boiled, stir-fried, or pickled.  I like to use colorful vegetables, such as broccoli, carrots, cucumber, cherry/grape tomatoes, snow peas, broccolini, red/yellow/green bell peppers, etc.  You also can shape vegetables using mini cookie cutters to add extra cuteness to your bento.
Umeboshi
A long-standing staple of bento, pickled Japanese apricots are believed to keep rice fresh and are served either on a bed of plain rice (resembling the Japanese flag) or stuffed inside onigiriUmeboshi has a very sour taste that is quite addicting.
Furikake
A condiment that adds flavor and color to rice.  Popular ingredients include nori flakes, shrimp, salmon, and toasted sesame seeds.  My favorite is yasai fumi furikake.
Seaweed
Included as stewed kombu, or wakame in a miso soup, or as strips used to wrap onigiriNori also is cut into decorative patterns, transforming rice into soccer balls, Sanrio characters, and other cute designs.
Fruit
I like all kinds of berries, tinned mandarin oranges, apples, bananas, and more exotic fruits, like mango, longans, and lychee.  If you pack apples or other fruits that tend to brown, try rubbing a bit of lemon juice on the cut surfaces to prevent browning.  Fruits also can be cut into appealing shapes with a paring knife or using small cookie cutters.
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