Hey I was about to respond to a thread about the usefulness of fuel cells, but then a quick double-check of TW/TM/TO/SO revealed that I didn't know as much as I thought I did.
What fuel specifically does a Fuel Cell run on? I'd always assumed it was a hydrogen fuel cell, but the structure explosion table in TO (p136) seems to imply otherwise, saying only that they're not ICE fuel and that they're simply "volatile chemicals". That same table (plus a fluff note in SO, p208 under Surface Transport) suggests that it isn't the same fuel used by an ICE, either. Tech Manual (p62, under Engines, last para) specifically states that fuel cells use two reactants (presumably the fuel and the oxidizer), but dances around saying what those reactants actually are. TO, p134 under Power Generators Table, says only that the fuel is liquid.
So what's a fuel cell actually "burning"? Hydrogen, plus an oxidizer? Petrol/Alchohol like an ICE, again adding an oxidizer? Or something entirely different?
This isn't purely a fluff issue. If they're hydrogen fuel cells, then they inherit all the rules for synthesizing liquid hydrogen as listed in Strat Ops p179. If not, then the question becomes, "Which entry do I use when replenishing fuel tanks?" per the Fuel Availability & Cost Table, p179 Strat Ops.
(Either way, while fuel cell fuel clearly includes an oxidizer, you could simply note that when purchased for fuel cells, the oxidizer is included free as part of the fuel cost/tonnage. That is, a ton of fuel cell "hydrogen" is actually only 100kg H2 and 900kg O2. The same if you go with hydrocarbon fuel cells. This way you avoid having the add a separate fuel cell entry to strat ops fuel prices.)