Rogues

a.k.a. duel-wielding rouges
(sorry, couldn't help myself, pet peeve)

There are two problems with the 'rogue' archetype in RPGs. One is the WoW-clone interpretation of rogues as just people who stab things... really, really hard. The other is the more basic D&D alignment issue, the image of rogues as flighty, shortsighted, and greedy.

As far as MMOs go, the problem isn't with the archetype itself but with the oversimplification of the genre. Rogue or not, all anyone ever does in a WoW-clone is stab things. Everything revolves around damage meters. In a real MMO, PvP would create much of the demand for the currently absent roguish trickery. Infiltration, distraction and sabotage should be the main purpose of a sneak, not just popping up to stab people in the back. Scaling walls, laying traps, disrupting spellcasting, relaying information about enemy movements or disabling mechanical constructs like golems or siege equipment should all take the place of simplistic stabbity-stabbity. Oddly enough, one of the most out-and-out copyish of WoW copycats in terms of gameplay, LoTRO, also features a delightful break in that pattern. The 'burglar' class in LoTRO is not a damage-dealer in groups. Instead, its purpose is to debuff or disable mobs, manipulate aggro and most importantly initiate group maneuvers.
In PvP games, the sheer 'OMG overpower-ness' of invisibility can quickly lead to the expansion of the archetype past stabbing. The main role of the rogue class in Savage 2 was to plant bombs by enemy buildings and to dash around forcing enemies to chase him. In EVE, cloaked ships were an essential part of corporate warfare as scouts. In TF2, spies are the bane of engineers, undermining both enemy defense and offense by destroying sentry guns and teleporters. Even in WoW, in the earliest PvP instances, i spent a fair bit of my time as a druid simply keeping an eye on enemy movements while prowling around as a stealthy little cat.

However, the problem predates WoW-clones. Computer RPGs in general suffer from limitations in the kind of flexibility which would allow for trickery, from an emphasis on simple brawling. Both rogues and mages are trickster classes but trickery is almost irrelevant when the object of the game is to kill everything. A frequent source of frustration is attempting to sneak around an encounter only to be interrupted and brought out of stealth by a cutscene. Other times the problem is that characters in a computer RPG always move together, which means rogue stealth is always undermined by less stealthy characters. Most times, there is simply nowhere for a rogue to use his skills. Even games which nominally include traps and pocket-picking only do so as an afterthought, with the rewards meaningless compared to the time investment, while scouting ahead means nothing because there is no choice but to kill everything to get to a boss anyway. Even if all the above are not true, even when it is posssible to steal, sneak or bluff one's way past encounters, the rogue's role is undermined the the outdated mechanic or experience gain and levelling up. Character advacement is at the core of RPGs along with moral decisions. When advancement depends on experience gained through killing, well... shoot 'em all and let the gods sort 'em out.
The one RPG i've played which truly integrated stealth was VtM:Bloodlines. Killing was only a means to an end, giving no experience or loot in itself. 'Trash' mobs were created to be bypassed. Many missions gave even better rewards if performed without ever killing a thing.

This also brings me to the second issue, that of true role-playing, the moral character and mentality of rogues. The main reason why stealth classes hold no appeal to me in most games is that they are treated as petty thugs, sneaking around mugging people for their spare change. One of the few breaks in that routine is Vampire: the Masquerade's take on one its vampire groups, clan Nosferatu, forced to continually remain out of sight because their appearance would give them away. I like the image of the Nosferatu as spies, information brokers and secretive masters of the underworld.
It's a quick reminder that James Bond is a rogue. In the real world, the sneakiest sneaks, the ones who can make all their bluff checks at airport security and always keep an eye on what porn sites you've been visiting, are kept in pretty tight check by various power structures like national governments and organized crime. They are brainwashed into obedience, unable to break away from whichever group has their nuts in a vise. They are Lawful, even if they don't obey the same laws as the rest of us, from Odysseus to ninjas to Mata Hari and the 007s of the information age. There is no reason why spies, brainwashed wind-up toys dutifully serving the whims of military or commercial overlords, should not play a much bigger role in games' stories.

Aside from that, it's the origin story of the rogue that always grates. Every rogue in fantasy games is a gutter-rat that was forced by harsh conditions to steal to survive, yadda-yadda chaotic good heart of fool's gold. Why not a trickster like a stage magician, certainly adept at the kind of sleight-of-hand that defines the rogue archetype? Why not a blackmailer, unable to sneak anywhere but trading information to get the upper hand on others? Why not an eaves-dropping courtier or a mechanical genius specializing in traps and sabotage instead of stabbing?