Of course, not everything "geeky" is part of a franchise. Choose the right color and your bento box could easily be mistaken for an old My Book-style storage drive. Blends right in on an office desk if you don't want to be conspicuous, and if anyone steals your lunch thinking it's hardware, at least you'll both be disappointed.
Another non-franchise option: the Book Bento. Something for your Tolkien and Jane Austen geeks, and holds more food than you'd think (I own this one). Also has a nice seal under the lid for slightly sloshier foods.
And why not bullet train chopsticks? Not everyone likes trains, but if you know someone who does, odds are that person is a geek about it.
Or you could go with this insulated Chewbacca bag available via ThinkGeek, and if you think that's cute and/or disturbing, check out Bonnie Burton's DIY Chewbacca tablet cozy. Arrrgh, gets me every time.
Incidentally, this Clone Wars item is called a Funtainer. OK! At least it's not a Thermal Jar-Jar.
Since we're talking about accessories, people who like an excuse to spend money collecting random little things LOVE bento gear. People who don't should run, now. The number of tchotchkes you can find to stuff in and around your lunch is near-infinite. For example, these Iron Man "Food Decorating Party Rings" are designed to be jammed into your food as decorating...party...rings. Yeah, I'm not sure either.
Dinosaur food picks are a bit more obvious: roll up a ham slice or zoodle stuffed with cream cheese, and stab it with a Parasaurolophus. Done.
Perhaps because most bento boxes don't have locking waterproof seals, they're traditionally wrapped in a cloth called a furoshiki (Batman-themed or otherwise). A drawstring bag with Superman, Super Mario or Dragon Ball Z does the same job at a lower skill level. This is the crafty sort of item people often put up on Etsy, with search terms like "bento bag."
There are lots of bento suppliers that ship gear out from Japan or resell from other countries, so if you want something, you can usually find it. The key thing is to make sure a box is large enough before buying. For tips and recipes, I like JustBento.com.