Standing at 177 cm with a rather lithe frame, Otacon is no bodybuilder- but he's not exactly a willow tree, either.
He has medium-long gray hair- he's been going gray since he was a teenager- which he doesn't normally spend much time up keeping. It's lucky if it gets a brush through a day, if that.
There are no tattoos or any unusual markings on him to speak of.
He keeps his fashion (if you could call it that) rather simple- a turtleneck sweater and jeans in colder days, and a t-shirt and jeans for hotter climes. And these clothes need not necessarily be clean, either- if it doesn't smell, it's alright with him. On occasions where he finds himself going out, he'll wear his old lab coat- he obtained it at Shadow Moses, and it's rather comfortable- why throw it away?
Finally, he wears glasses- the man is terribly near-sighted (almost to the point of complete blindness for anything a foot or more away from him ) without these lenses. He doesn't wear contacts as even the sensitive ones make his eyes rather uncomfortable.
Otacon is a soft-spoken, timid person. He tends to keep to himself more often than not, usually through something on his computer. Or, if not his computer, it'll be a video game, or anime- in other words, your stereotypical "geek". This belies his other traits, however- the man is a technological genius, and tends to stick around his machines. He finds it difficult to interact with most people, since they're "so illogical", and holds a fond love of computers and robots, which goes along with his other love of Japanese Animation. In fact, his alias is derived from the annual Otakon (Otaku Convention), of which he was a regular participant of.
It was this love of animation- and robotic animation in particular- that drove him to be a participant in the Metal Gear Rex project in the first place. Note also that he hates his given name. He was named after the computer in 2001: A Space Odyssey, which he can't stand, and prefers that people call him by his alias.
Otacon has a habit of pushing up his glasses when he's nervous- or pleased.
He tends to have a certain sense of intellectual hubris, especially when it comes to topics he knows about, and will gladly give information about anything questioned on (often times at great length if it's a topic he especially loves)- much to the dismay of others.
He has a strong sense of morality, despite his past- he firmly stands up for what he knows is right, and can be rather stubborn in moving away from that ideal unless you have hard proof saying otherwise.
Despite his feelings towards people as a whole, he makes attachments very quickly. Once he's gauged that you are a "good guy", he'll stay by your side no matter what- issues of common sense aside, of course.
Otacon also tends to have a deep sense of guilt- his actions in the past and present alike. Should he fail at something, he tends to beat himself up rather harshly about it. Along those lines, he will step up and take responsibility for his actions (or lack thereof), and do everything he can to rectify the situation. He tries to atone for his sins, no matter how small.
Finally, one might get the impression that Otacon cries a lot. This is not the case- despite his insistence that he isn't, Otacon is a very emotional person, and cares deeply for what little friends and family he has left (namely, Snake). He's not above crying if something particularly moves him- and, most recently, it was his sister dying in his arms.
He also seems to have a difficult time interpreting proverbs.
As mentioned, Otacon is a technological genius- having a Ph.D in Engineering helps to prove that point. Given the bare amount of tools and enough time, he can build a variety of miniature robots to take care of menial tasks- currently, he was working on a remote-controlled robot with data feedback, but the technology just isn't there yet. Robots aside, Otacon has enough skill to repair (or at least do a patch job) on most mechanics out there- elevators, computers, cars/bikes, you name it.
Along with his handiwork with tools, Otacon is an amazing hacker. Give him a few moments, and he can hack his way in - or out, if need be- any system in the world. He tends to navigate through computers as a fish moves through water.
Unfortunately, Otacon is not the most physically capable person in the world- he can barely lift 30 lbs without straining himself. All the work and effort into broadening his mind hasn't been great on his body, and he's at a severe disadvantage with it comes to any physical contest- friendly or hostile. He was taught by Snake on how to use a tranq gun, but his aiming his terrible since his hands tend to shake, and he never remembers to bring it with him. This isn't to say that the man won't try to defend himself should it come down to that- but he won't be especially effective.
Along those lines, he's a terrific klutz; often losing his balance, and will literally trip over his own feet if he's nervous enough.
One very severe weakness is that he's loyal to a fault. Distrustful enough at first, should someone manage to win his loyalty (or affections), he will stick by them to the end. This is caused him some terrible problems in the past, but either he doesn't realize the reason why, or he chooses to aptly ignore it. Someone with this kind of knowledge could do some real damage via Otacon.
Glasses aside, he always carries his laptop when he's out and about- mostly for missions, but also to quickly gather information or jot down notes.
There is one other item that Otacon keeps close to him- Snake's dog tags. They were given to him by Snake shortly after the Big Shell incident- he was told to hold onto them as "insurance". Otacon's not quite sure what that means- and he hasn't gotten the courage to ask just yet- so he keeps them around his neck, hidden underneath the layers of clothing.