- That's the waste product!! You can use (typically) hydrogen, methanol or ethanol to feed a fuel cell. Water can be used as a fuel, but only if you split it into H2 and O2 first - which obviously takes more energy that the fuel cell delivers in electricity.
Hydrogen is bulky and heavy to store and perceived as dangerous but makes for quite efficient power conversion. Methanol is easier to store but poisonous. It's difficult to get good efficiency. Ethanol is easy to get hold of (ferment anything you like) and is already part of the distributed fuel chain. However, ethanol cells are in their infancy. All can be environmentally neutral, ultimately simply releasing recently stored solar energy (unlike many so-called environmentally friendly electric vehicles which for the large part just move the point of pollution further up the chain)
Given the huge investment going in to fuel cells we should see some significant steps in the short and medium term. The problems (and I'm sorry to say I'm merely a bystander in this) seem to be around the catalyst that promotes reaction.