The majority of hydrogen production right now is done through steam reformation of natural gas. The only by product is C02 which is obviously a greenhouse gas but is much better than C02, Nx's and hydrocarbons. The combined efficiency of reforming and the FCV should be alot higher than refining and an ICE engine.
The thing is there are pathways to make zero emission hydrogen. Powertech out in surrey has a stuart power electrolyzer to supply the hydrogen for their vehicles.
When things get going methanol will also be reformed for hydrogen production and then at some point the direct methanol fuel cell should become available.
http://www.bellona.no/en/energy/repo...999/11193.html