Is there anyway that I can make her gain her confidence back?

She must be going through a tough time I suppose. Something must've ticked her off while you two weren't dating. Sometimes me as a girl (I take how I look personally). and if someone says something to me I would just look at myself and think yeah I guess I am ugly, or not beautiful like christina aguilera or pamela anderson. But besides the point, I know how your girl feels, its hard for someone like her to be in this situation but eventually she will realize that she really is beautiful and she will be confident of the way she looks and her body.

When she is saying these things, just hold her and say "everything will be okay, I'm here for you"
Tell her YOU like her just the way she is. A girl likes to hear these things from guys. especially someone they care for. Hold her tight until she is feeling good! that is my best solution. I would love it if a guy would say those words to me.

Wow! Something must've happened to her.

Thats a really tough question to answer. I would say that you should try to talk to her about it - about what happened. If you're in a relationship where it would be alright to talk about it of course. You don't want to get too up close and personal after a breakup. Go slow, I think telling her you think she looks great is a good move, but also let her know, that she has to feel great too. Encourage her to tell you about things that make her uncomfortable and loose her self-confidence. Its also a question of her hobbies. Doing things she likes, and she is good at are an ego booster that might help.

And maybe, if you guys are into that, go to a club outside of your town, where it is unlikely that anyone knows you two, maybe pointing out to her all the people that are being friendly to her, can help her see that other people like the way she looks, and is, as well.

Make sure to be specific and logical in your compliments. Don't just offer compliments, explain them in detail. Girls know that sometimes guys lie to make people feel better, get in their pants, be nice, etc. When you explain the cold hard logic of it all, then it is undeniable. You said she's getting better, so it's not a lie, so take the effort to figure out how and why she got better and tell her.

As for continued gains in confidence, I can't tell unless you explain what it is that was/is wrong with her body and appearance.

Wow. I know you said it more for girls to answer but, I thought I'd throw my opinion out anyway. Obviously something happened between those 6 months or those 4 months with another guy that caused her to become overly self-conscious about the way she looks. If that jerkhead she was with had expectations of her body and verbally let her know that she needed to change, that would definitely cause her to become less confident about herself.

Again, I'm not a woman, but there are some things that just seem right that you could say to her. Maybe she is just waiting for you to mention it to her. How about, "What are you talking about?!? You are freakin hot!" or "I can't believe you think you are ugly/fat/ect., because you rock my world!" "I can't believe you actually like MEE!"
You know just completely blow her mind and all of her insecurities out the window.

After saying that, if you guys are close enough, you said you have been together for almost 3 years now, so why not just kiss her and offer to give her a massage or something. Everytime she brings it up, hug her and softly tell her that you have no idea what she is talking about. Women can be very insecure about themselves, so they need extra attention by their guys to tone down those negative feelings.

I hope you guys get back the way you once were! Good luck!

-Shyyz