This is a really tough question. In my experience there is no one solution to this problem. And every woman feels differently about it. But the most difficult thing is that no one can force anyone to feel pretty. No amount of compliments or anything will make her believe them. She has to figure it out herself, which sucks, but it's the most sure fire way to get confidence to stick around.
I wish I had more ideas to help you out.
The one thing that I appreciate a lot is when my husband notices little things. I much prefer 'Your eyes look amazing today.' Or 'I love what you did with your hair.' over just a general 'You're pretty.' Noticing the little things, to me, means he's actually paying attention and I like that.
Is weight really an issue? If it is an issue, I think doing a dietary change together might help. That way, she won't feel like you're telling her she's not good enough, or that you're unhappy with her appearance. Eating better also has other pretty snazzy side effects - more energy to do things, your body will feel better from the inside out, and with feeling better maybe even some confidence will sneak into her life.
Man, I feel like this is about to get long-winded. Brace yourselves.
I struggled, STRUGGLED, with weight and body issues for years. And nothing helped. Even going to doctors did little to cure me. Sure they got me over my social anxieties and depression, but my self hate stuck around. Being at collage was both the best and worst for me. I basically lost everything important to me in matter of a couple months and when I was the most alone was when I figured it out. I figured out my own self worth and what I did then is what I continue to do now: I will never weigh myself. Ever. Society puts a lot of pressure on the numbers when really, they shouldn't matter. Everyone is all wrapped up in 'You should weigh this much, or you're not good enough' blah blah, whatever. And so, I don't own a scale and I don't see their importance. That may be completely the opposite for you wife - maybe she likes to see numerical progress that she makes? But really, not having a scale helped me a lot to not give a damn about the numbers.
I feel like I have a lot more to say about the subject, but I don't want to get rant-y. And I would.
Continuing to be supportive is key and I hope your wife can find confidence in her self someday soon. It really just kills me that women can't wrap their heads around how pretty they are! Everyone has their crappy days, but seriously, I have yet to meet someone who I don't find gorgeous.