I'd like to reopen this conversation now that ModLoaderMp has a proper addFuel hook that takes metadata into account, meaning this is actually possible now.
Filled Fuel Can should 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.