But really, despite what "Demon" claimed, obtaining deuterium in space isn't hard at all. There's always going to be plenty of the stuff floating around. No need to devise convoluted ways of obtaining something that's all over the place.
...Until you get so low on deuterium that hunting for more deuterium is going to cost you all the deuterium you already have, and then some.
Which seems to be what happened in "Demon". Janeway was betting on getting highly concentrated deuterium, so she didn't hunt for the dilute stuff in interstellar space. But she got denied too many refueling opportunities in a row, and finally was flying on fumes, past the critical point where said fumes would allow her to gather more deuterium than she burned.
Transmuting elements is decidedly a capacity a starship possesses in normal conditions - in TNG "Night Terrors", loss of said capacity was considered an emergency. However, transmuting elements for fuel may well be futile, in the sense that no fuel one could hope to create that way would release enough energy to compensate for the effort of transmuting.
Now, creating
anti-elements seems like it could be worth the effort. Backstage material claims that 24th century tech can do that pretty efficiently: by expending ten units of deuterium, one unit of antideuterium is gained. And that's pretty nifty magic, because annihilating that one unit of antideuterium will liberate more power than fusing of those ten units of deuterium would have liberated. (Although the TNG Tech Manual is fuzzy on the details, it's obvious that those ten deuterium units aren't expended in annihilation, because the whole purpose of the exercise is to create annihilation fuel where none existed before. Apparently, the ten units are expended in D-D fusion of some sort.)
Of course, that's just backstage talk, and never verified onscreen. But if it's true, then it's obvious that a starship could operate simply by gathering deuterium and never worrying about antideuterium. What Kirk says about "power regenerating" in "Mark of Gideon" might be quite true, then: the ship would in theory fly forever. Assuming she flew through dense enough deuterium clouds, that is.
Probably there just isn't enough deuterium in space to keep the process on black ink, though. So all starships rely on pit stops at reserves of concentrated deuterium, and those only exist at star systems, many of which are off limits.
Timo Saloniemi