|There are significant exceptions, which are interesting because they are so exceptional.|
For roleplaying, it doesn't work so well. Usually, damage in roleplaying games is abstracted into hit points, which may include physical body survivability, but which is mainly representative of the heroic hero style of combat where fists and swords and bullets constantly just miss, or barely nick the clothes, perhaps breaking the skin enough to shed a drop of blood. As things get worse, there can be lost teeth, black eyes and bruising. Sometimes a continuing fight needn't even be that obvious about who's losing, with heavy breathing or a sweaty brow enough to make the point. All of this is mere visual effects, a way of indicating which way a fight is going for each participant, before eventually getting to the final bottom line: Does someone get a sword in the gut or a bullet in the brain, taking them out for good? That end result may be the bottom line of the fight, but it's not the story of the fight, and roleplaying is all about story. (Or to put it another way, the statement, "Ali beat Foreman", just isn't very exciting on its own.)
That's what the bland Hit Point stat in most games is meant to stand in for, especially heroic games in the D&D style, where hit points can just keep growing and growing, no matter how constant the character's physiology remains. Not all players think of it that way, not all GMs explain it that way (I personally like to drop in a few cool special effects when I can see places for them, but otherwise leave it to players to fill in most little details like this in their own manner), but it is what the number is technically meant to represent. This doesn't fit too well with the Boolean efficiency of a typical Star Trek phaser fight. Sure, Kirk can pile on the visual effects for ages in a sweaty, topless fist fight, but as soon as someone pulls an energy weapon, the style of the fight completely changes and it's mostly one hit, one stun/kill. Forcing the phaser's efficient stun setting to fit in with the flowery fisticuffs rules seems to miss the point.
We found a similar issue with Stargate roleplaying and the zat. On screen, that has a really clear set of rules: One hit stuns, two hits kill, three hits vaporise. It's perhaps not the most realistic rule, but the series sticks to it pretty consistently, and then the roleplaying version of it utterly ditched this to force the initial stun shot to comply with more conventional roleplaying combat rules instead, with much more drawn out Saving Throw rules complicating the process.
Of course, instant kill weapons are not unknown in all roleplaying. Some systems (I can't think of an example right now) may explicitly run damage that way, while some like Call of Cthulhu and Warhammer simply keep the weapons damage pretty constant and hit points constanter, and both approaching the same average figure, so that survival is possible, but not inevitable. Getting shot once is probably a terrible thing.
And it would certainly simplify any Star Trek roleplaying system if the whole energy weapon damage scheme boiled down to definitely stunned, wounded (roll for how much), definitely dead (with corpse) or definitely dead (no corpse).
Trouble with instant take-down is that it doesn't lend itself to all kinds of drama, and certainly not the sort that players prefer. Players like their characters to participate, to stay conscious, to carry on from session to session, giving some sense of personal continuity. Outside of silly things like Paranoia or Kobolds Ate My Baby!, PC death is accepted to a point, but not when it's down to little more than a coin toss every time they step outside.
From the GM's point of view, it also becomes difficult to justify why villains wouldn't love such instant take-down weapons. Sure, maybe a Klingon warrior enjoys honourable combat enough to want to use a bat'leth for slower hacking and chopping, but a more to-the-point Romulan or an aggressively obedient Jem'Hadar would surely want to dial their shooter up to 11 and get some killing done and over with. Yet from a storytelling point of view, the GM controlling such NPCs needs to balance such motivations against giving the players a fair chance at survival. Some GMs would worry about that more than others, but it's still got to be a consideration. It was a bizarre oddity in our recent Dominion War campaign that it was more often the 'vicious' Jem'Hadar firing weapons set to stun or low damage, and the 'peaceful' Starfleet officers always looking for the vaporize setting and rolling buckets o' damage dice.
Part of the problem, perhaps, is that this all follows the standard D&D model, and in D&D the monsters come pre-built with different amounts of damage at different levels. In Star Trek, a starting character is as likely to face a weapon with a Maximum Super-duper Kill setting (because it's such a common thing that a weapon without it would take a lot more justification, every damn time) as a very experienced character, and all that usually changes is the competence of the weapon's aimer.
The bottom line? There is none. I'm not sure what a reasonable, workable solution to this is. I'm open to any and all thoughts. Begin!