I completely agree that the "skinny" jokes they are making at you are just the same as "fat" jokes. They are bullying you plain and simple and that is not okay, whatever the motive may be.
Like you, I'm very thin with a very high metabolism. It's the way my body works. It's scary sometimes because if I get sick and lose weight due to illness, it can get dangerous really quickly. I have to eat 3000 calories each day just to maintain my weight. I'm a nursing mom, which drives up my metabolism even further.
My boss, who I love, was making a bunch of comments about my weight, and it was really bothering me. Unlike your friends, she wasn't trying to be mean. She thought she was being complimentary. I finally had to say, "Please stop commenting on my weight. It makes me really uncomfortable." She stopped immediately.
I would recommend a similar tactic with your friends. The next time they say something, say, "I don't make jokes about your weight. Please don't make jokes about mine as it hurts my feelings." If that doesn't stop it (and from the sound of the dynamic it may not), then it's time to get new friends.
You deserve better than to be hounded and bullied by people close to you. You are worth more than that. You shouldn't have to feel sad and guilty about your body. I actually just wrote a blog post about this very thing. Maybe it will help you:
http://knockedupknockedover.wordpress.com/2012/06/28/bein...
Another good resource is The Body Is Not An Apology:
http://www.thebodyisnotanapology.com/
(their facebook page) http://www.facebook.com/pages/The-Body-Is-Not-an-Apology/...