I don't really understand why this isn't already implemented, but Filled Fuel Can should really work in vanilla Furnaces. And by extension that would allow them to work as fuel for any mod. *cough* Railcraft *cough*
Modloader has a hook for this. As it stands, if I want Fuel Cans to work in my Tunnel Bore, I'm going to have to write some custom code for it.
Also, I haven't checked this, but if Filled Fuel Cans don't have Empty Fuel Cans set as their container item, they should (like buckets do).