I say antimatter, but TOS and Voyager say otherwise.
And TNG. In "Peak Performance", Riker's ship didn't have any antimatter at all; then Wesley transported his science project over; and then the ship did have antimatter. Also, shuttlecraft were to be transported in some cases such as "Deja Q", although we could argue that those aren't necessarily powered by antimatter.
TAS, too. And ENT, in "Civilization" at least. And I'd really be surprised if DS9 didn't have a reference as well.
It would be interesting to learn how antimatter is transferred from stores or tankers to starships. Which is riskier, transporting or physical moving?
Not to mention an absolutely faithful brain. If I'm not mistaken, Trek--in a workaround fashion--wound up positing a quantum component to consciousness before Penrose did in order to account for the inability to replicate minds, but the substrate on which conscious works is at lowest level a molecular pattern, and should be totally replicable...
I don't remember any references to minds being unreplicable, really. It just isn't done (onscreen at least), but it's not labeled as impossible, either. Certainly living neural tissue is replicable, as in VOY "Emanations".
As for differences in taste, well, they are likely to be differences of taste. That is, two identical dishes may always be deemed different if the guy doing the deeming is intent on deeming that way. Probably there's no difference between replicated Chateau Picard and the stuff that Robert used to grow, but nobody is going to admit that, at least not within an arm's length of Robert. It's probably just as fashionable to say that "real" wine is better than replicated as it is to say that wine X is better than wine Y - completely subjectively, without regard of measurable facts, and typically also with an agenda.
Timo Saloniemi