I have a younger brother, he turned 16 in November and he's been my ultimate best friend since I can remember, we've had sibling fights but I love him to pieces.
Recently he's been acting really cold to me; he'll not join in when I'm trying to have a laugh with him, he'll say "Shut up." "You're annoying me." "Get out." and stuff when I'm talking to him or even in the same room watching something on TV and it's making me really upset :( And he's started being violent towards me; he plays rugby and has big muscles and he's at least a foot taller than me, he used to hit and punch me as a joke (he doesn't know his own strength) but now he does it with malicious intent.
I know it could just be him being a teenager but it's making me unhappy.
How do I fix this? I've asked him about it and every time its "Get out, you're annoying." I don't know what to do, we were so close but now it's like he wants nothing to do with me.

I realize you have had problems in other areas of your life. I realize you "fake" illness as an attention-getting device - does this cause him to be largely ignored and does he resent it?

Is he the same brother who was overeating and food had to be locked up in your house?

I think what is happening now is a symptom of other, deeper issues.

I don't fake illnesses anymore, I haven't since I was 13 and he used to make fun of me for it; and he is the same one that was eating everything.
I don't know how any of that would relate to his behaviour now though? I thought it was just him turning into a teenager.

Aside from issues already brougt up, which could still be related, some other things to think about - you mentioned he's an athlete and aggression like you are describing can be caused by steroids - any possibility he's using them? It is also very normal for boys his age to want a lot of time alone, and to find family annoying even when the family isn't being particularly annoying per anyone else's opinion. I'd recommend you give him his space - if you respect his preference to be left alone and let him seek you out when he's in the mood for famliy and company, he'll come around in time. You shouldn't tolerate him hitting you -tell your parents it's going on.

Sounds like there's a lot of discord in your house and your brother may just want to distance himself from it. Avoid making drama and attention getting behaviors, etc. that might drive him and others away from wanting to be with you.

Our home is quiet now.
Me and my brother were always together when we were younger because we were both afraid of being told off by our dad (we aren't anymore, we love him again) so its just weird to me that he wants to be separate so much.
And there is NO WAY he's taking steroids. For a start everyone would hate him. We live in the English country side, there's only 750 students in our high school and everyone knows everyone else's business. He wouldn't get away with it; also he isn't stupid, he's never smoked and thinks drugs are for the lowest of people.
I am leaving him alone, I'm a bit lonely but I don't want him to hate me. He told me last night some of his oldest friends (as in he's known him for years) have ditched him and he doesn't know why but he assumes they think he's 'horrible' which I know he deffinately isn't. I would have thought that would make him want some company :(

I'd recommend you just tell him you sense that he wants his space but you miss spending time and being closer with him, and hope that he'll let you know if he wants to hang out with you. Then let him take charge. He could be depressed or something - apparently if he thinks his friends hate him, something's going on with him. Ask perhaps why he thinks that, and if anything in particular happened.

Sometimes around 15 or 16, people start separating from the friends they had from earlier years of school and start forging new friendships, not because anything happened but because criteria for friendship changes as we mature. Living on the same block and being the same age may be enough to have in common for younger kids, but older teens need more of a connection and seek friends with similar interests. That could be happening where your brother's friends are finding people who are more in line with their interests, but he hasn't found his crowd yet - it's very hurtful but when he finds his right crowd, he'll be happier with them.

He has a lot of friends, I didn't mean for him to come across as 'billy no mates'. Its just the ones that live in our village; because of where we live it takes at least 20 minutes to drive to the next town over where our other friends live. I'll talk to him, to at least let him know I'm here for him.

He's going through the same thing a two- or three-year-old goes through as part of his personal development -- he pushes away his family and wants to do things by himself and doesn't want to be told anything. In psychology, it's called separation and individuation. It's normal.

Like someone else mentioned, just let him know you love him and are there for him.