It's been over a year since I read Wind-up Girl, with many books between then and now, so my memory is kind of hazy... but thinking back, I can't remember any electrical energy in that world. Was it all mechanical? If it's all mechanical (for whatever reason), that really limits what sort of energy sources are useful. Especially portable energy sources. Most current energy sources, green or otherwise, are to produce electricity. I'm have no idea why (if I am even recalling correctly) electricity doesn't work, but it would only take a sentence to reasonably dismiss electricity entirely in a sci-fi world. You can write that sentence for yourself in your head while reading, if it doesn't exist.
Of course one thinks first of steam, for mechanical power. But what do you burn to get steam? That's a problem. Also, while the oceans are still abundant, fresh water seems like it might be kind of dear in that world ... at least so it seems, as I'm recalling the torture the Windup Girl undergoes constantly trying to get water to keep herself from overheating, and it not being easy to acquire.
It should be noted that Windup Girl takes place in a world already mostly established by Bacigalupi in his short stories in Pump Six. Pump Six is a collection of short stories. Windup Girl is sort of, in some ways, like a really long short story. Not everything is explained. (I think Pump Six is a significantly better work than Windup Girl, though Windup Girl is still quite well done.)