More less obvious choices!

Most quests in computer role-playing games are not truly optional. You either do the job or you don't get paid, don't get your experience points and miss out on the interactive content you bought to boot. You don't get the option of stabbing that NPC in the face for even asking you to perform such heinously bland deeds, or siding with the opposition, keeping the macguffin for yourself, etc.
Of the fewer branching quests, most present one blatantly obvious right choice conforming to prevailing mores which also gives better rewards. Saving the princess just pays better than selling her into slavery.
Only rarely are we presented with a true practical and roleplaying choice.

By the by, this will be little more than a slew of spoilers about the outcomes of a few RPG quests, so if you're squeamish about that sort of thing, skedaddle. G'wan naw, git!

Anyhoo.
The practicality of RP choices in terms of gameplay mechanics, rocket launcher or laser gun, monkey grip or great cleave, the carrot-and-stick, cost-to-benefit or risk/reward estimates are a subject in their own right. For now I'm not particularly interested in the endorphin titration of the promise of cake. I'm thinking more of the few instances where we're really faced with aesthetic or moral options, with a choice between two actions, most often both appealing and despicable, where the player's own self-image, own demons, discrepant Jungian anima and shadow, are projected into the activity.
Before getting into RPGs per se, good old Half-Life offers a most concise and accessible example of such externalization. As you (incarnate Gordon Freeman the MIT-educated physicist with newly-discovered survivalist aptitudes) stalk and bumble your way through the game's various area-fifty-somethings, you run across other survivors of the Black Mesa disaster. They're helpless or nearly so, your fellow eggheads in white lab coats or the complex' underpaid, overfed and nearly-competent security guards nicknamed "Barneys" by the developers. Some are involved in the game's action but most are mere window-dressing and as such eminently disposable. So will you save them from marauding alien hordes or watch them get butchered... or put a bullet in the back of their heads yourself? Are you a benefactor, opportunist or petty sadist? And more importantly, would you-as-Gordon, not just the roleplayer but the role being played, feel any kinship toward these poor two-bit (8-bit? 16-bit?) schmoes?

Very few games can make you feel as though you're not simply going through the motions, as though you truly do have a choice to make. It's a matter of atmosphere, pathos and balance, but most importantly you must know your audience in order to offer truly competitive options. I am now on my third playthrough of Dragon Age: Origins and I have never, not even when I was palling around with Leliana and Alistair, promoted the building of a chantry in Orzammar. Be I mage, Dalish or dwarf, no incarnation of me could condone the spread of organized Chanting.
Ah, but what of Andraste's ashes? No mere object of worship, that, but a piece of history, a cultural icon, a valuable object of magical study. I would no more defile the ashes in Ferelden than I would whitewash the Sistine Chapel in real life. When you can write choices so poignant and weighted into your role-playing, when you can make a rabid anti-theist protect a religious artifact of his own free will, you're obviously doing something right.

But of course Dragon Age did not do everything right, so before moving on to other games, I'll run through its better and worse examples.

Dragon Age: Origins

Orzammar: the dwarf mage and the dwarf chantry quests are presented as separate, but address the same issue of small beginnings of change within dwarven society, progressive and regressive respectively. Unfortunately they're both presented as chores not choices. Do the job or don't get paid. Both could have been more interesting with just a bit more leeway for player input.
The Bhelen/Harrowmont choice is again interesting morally. Tempted as I might be by Bhelen's promise of change, I could not bring my elvish self to side with an underhanded power-hungry Cassius-type. Chalk another accomplishment up for DA:O's writers, getting me to throw my lot in with conservatives.

Speaking of elves, I tend to always play one... mostly because I can't play a werewolf in these games. The most sinister, mean and dirty trick DA:O played on me was giving me both wolf-men and elves... then making me choose between them. My babies! Nooooooooooo...
But I'll bet I'm not the only one. Many of us escapists identify with both the ostracized freedom of lycanthropy and the noble, holier-than-thou superiority of Tolkien's elves. Pitting our conceits against each other was a wry show of mastery of their chosen field of expertise on Bioware's part. I don't often opt for compromise but so help me, caught between the Dalish and the Brecilian werewolves I really, really tried.

Of much lower quality was the choice between mages and templars in the circle tower. Too much whining, too much pressure to play savior was put on the player, especially during the conversation with Wynne, to make this a valid choice (though Morrigan, bless her wild heart, if brought along cuts right through the treacle there.) Though the strategically sound option would be to carry out the annulment, too many lines of dialogue make it clear that you're expected to play hero.
I mean, I would've sided with the nerds against the jocks anyway, but I resent being peer-pressured into it.

Before moving on to other titles, back to Orzammar for the end of the golem storyline. It's very interesting to actually be allowed to make the choice normally reserved for comic-book supervillains: acquisition of a superweapon by intrinsically unethical means. Normally players and viewers are always limited only to the facetious moral absolutism of stopping any action which might violate social mores, regardless of benefits. Having now played both sides of the quest, I'm very happy with how carefully the moral implications of golem manufacture were weighted against military pragmatism. This is how the Circle Tower quest should have been presented.

Neverwinter Nights 2
NWN2's original campaign was too simplistic to offer much real choice, though the courtyard buildings in Crossroad keep were interesting. I've been hoping to see more cross-pollination between RPGs and city-building strategy games and it's a pity we don't get to choose the composition of our redshirts or the construction of our evil lairs in RPGs more often. Practical considerations of mages vs. knights aside, there's a roleplaying choice to be made there. My chaotic neutral halfling druid would much sooner have co-opted an extraplanar wizard than the local praetorian guard.
Only in NWN2's story-oriented expansion, Mask of the Betrayer, do we find some hint of what was to come in DA:O, with Gannayev foreshadowing Morrigan and One-of-Many... noone. That'd be one of my complaints about DA:O. Aside from the Brecilian wolves (and that only an aesthetic choice), you don't really get a chance to leash something dangerous, to bind wild and malefic forces to yourself. The choices linked to One-of-Many's acquisition and further appeasement were the closest Bioware's came after Planescape:Torment to the gut-wrenching temptation to truly play an evil character or the associated guilt.
Speaking of which.

Planescape:Torment
Despite its very involved dialogue interactions, Torment offered surprisingly few evenly-matched choices, in retrospect. Mostly, they are linear tasks you must perform as-is to the best of your ability scores. Self-interest and the continuation of the game experience were predominantly allowed to overshadow morality. Take for instance the Grimoire of Pestilential Thought, which could have made for a very interesting quest line if its rewards were not so anemic as to make sacrificing companions pointless.
The kicker though was the ability to go the extra mile while getting your reward, to kick a few NPCs while they're down, to call a prostitute a whore instead of graciously avoiding the topic or poison a deadbeat barfly to death.
For an actual choice one might look at the two factions of the catacombs, the Dead Nations vs. Many-as-One. Do you promote a necropolis with its cadre of subterranean flesh-eating ghouls or a hive-mind which will likely rise out of Sigil's ground one day to gnaw on the populace?
The few times you do get to choose, it's between two evils. Most of the time, all you can do is express regret as you perform your grim deeds.

Vampire:The Masquerade - Bloodlines
Last, but never least.
Though a bit more flexible than Torment, Bloodlines followed much the same pattern in shaping the player character's identity. Evil is all around you and unavoidable and you yourself are inescapably an evil, destructive creature. You do however get more choice to perform small kindnesses... or not.
The best example of Bloodlines' brilliance in this respect is Heather Poe, the girl found wounded in the hospital and your personal blood-bound slave afterward. Though it's quite possible to do right by Heather and not drag her down with your sorry undead carcass on your way into the gutter, the game quite persuasively baits you into keeping her bound to you... until it's too late.
True choice was however still available only in token amounts, notably in the "Sibling Rivalry" quest early in the game. Both Therese and Jeanette are annoying in their own ways, and I found myself seeking a compromise because I didn't particularly want to side with either.

I suppose all this is a point in favor of large companies. Though I still hold both Torment and Bloodlines in higher regard than DA:O, I can't deny they fall short of it in this respect. Smaller companies, free of much bureaucratic bottom-lining, are much more free to indulge in true quality, in atmosphere and nuance. I don't doubt the older games' development staff were capable of creating evenly matched alternate choices, but truly branching storylines imply a redundancy of content which does not necessarily provide a timesink to make customers feel as though they're getting more for their money. A smaller developer cannot absorb the cost of creating multiple sets of backgrounds, animations, writing, voice acting etc. for each single quest, much less testing and balancing all that. Whatever Origins' budget, it was likely an order of magnitude greater than that of Torment or Bloodlines. Of course any company rich enough for that is much more likely to market to the lowest-common-denominator instead, making all those quest options truly irrelevant.

Makes me really, really antsy to see how inXile's going to use those four mil $$$ they wrangled from us through Kickstarter... and makes me wish DoubleBear Productions would kickstart its own project. We need the people who created Torment and Bloodlines to get Bioware-sized funding. We need more tough choices between wolves and elves.