I've separated some titles into somewhat arbitrary grouping. I list each in order from most memorable to least. This could go for the game's story, mechanics, mood or otherwise.
Story Driven Branching Path RPGs:
This category tends to fight with what Sui Generis is going for, but I figure it deserves a mention anyway. Even if it's an overly simplistic way of presenting 'choice' (as so often these kinds of games make choice more an illusion than anything else) they can still serve lessons in how to present plot, character motivation, game mechanics, et cetera.
Neverwinter Nights 2: Mask of the Betrayer
Although it's source game and predecessor, Neverwinter Nights 2 & Neverwinter Nights were both well enough, Mask of the Betrayer really hit it home. For a typical branching paths multiple choice game, Mask of the Betrayer allowed a lot of content to be skipped by choices early in the game, and many diverging paths by the end based on a huge handful of choices made throughout. While there are technically only three types of endings, they each varied considerably within themselves based on actions taken throughout the game.
Knights of the Old republic 1 & 2
The KOTOR series is still one of the only RPGs that I felt had its supporting cast of characters evolve along with the player's actions. Friends and allies would become more kind or sadistic, especially in KOTOR II, based on their influence and alignment of the player's actions. While the main plots tended to play out the same no matter what choices were made until the very end, there was a great deal of unique and thought provoking side-quests which spanned over several worlds and gave a feeling that the plot wasn't just separated into chunks like many other RPGs.
Dragon Age 1
Especially on harder difficulties, Dragon Age really required a lot of coordination and tactics before challenging battles. Synergy between rogue and mage character classes became a big help, and allowing new class options to unfold along with choices made during the plot was of great interest at least to myself. While still sectioned-off, even major and minor interactions with NPCs could be exploited or left alone for interesting rewards. While the consequences of choice weren't always felt throughout later parts of the game, the sheer number of divergent choices that had at least some impact down the line made for a great story experience.
Mass Effect series
Mass Effect really won out in its presentation and polish. It was not exactly innovative in any of its mechanics, but the cohesion of its story, believability and reactions of its characters, and consistent reward of the player for any style made it stand out.
MMORPG:
It might seem like this section doesn't really belong in relation to Sui Generis at all, but I think some of the titles I mention actually have more in common than at first glance. What makes a good MMO is at least the illusion of a living, non-static world, which some other RPGs fall back on.
Star Wars: Galaxies
Before the dreaded 'New Game Enhancement,' SWG was revolutionary in my eyes in that you really started from nothing. You were worthless and could hardly fire a blaster straight. You earned every single inch of prowess you had. It really was a Star Wars 'simulator' and brought a level of realism to MMORPGs that isn't often seen. While the NPCs were fairly static, that was made up for by leaps in bounds by the player-driven economy. If you wanted something, chances are someone had to make it, and for them to make it, someone had to mine the materials for it and even then, someone had to build the mining equipment. Everything worked on a schedule as well. If you wanted to travel to another world, you had to wait for a shuttle to actually arrive and buy a ticket (before player ships at least). I could go on about player cities as well, but that's a bit too far outside the scope of Sui Generis.
Everquest
What was amazing to me about Everquest was that you had to literally type every question out to NPCs. No predefined answers, you had to Hail an NPC and based on context clues in their responses, you could type out and ask them about a huge number of topics. It made the experience of getting assignments extremely satisfying (and improved proper typing skills and grammar to boot)! The User Interface was probably one of the most immerse I've come across. Want to give an NPC an item he asked for? You had to literally drag it out of your inventory and hand it to them yourself. And don't even get me started on the maps! I made a role-play adventure out of map-making using the in-game feature with a friend for almost a solid month! It's all these little things that added up to an ultimately basic game, but made it truly immerse and fun.
Everquest 2
The second installment of the series differed radically from its predecessor. Conversation with NPCs had options, but they were arbitrary at best. However, the world had built up a -lot- of lore thanks to its previous incarnation. Because of that, every piece of architecture had history, there were a thousand 'heritage' items with long quest chains that all related to items from the previous game, and the world was under a very cohesive general mood: the apocalypse had already happened and he gods had left. Everything about each new area drew back from that main theme and it kept the world very well grounded no matter the stage the player was at. The plot was never centralized, and you could skip entire areas if you outgrew them too quickly. The game mechanics were still very basic MMO fare, but the narrative of the game was so well grounded in every aspect that you had to try to ignore it. This was also the first MMO I had played where they attempted to give NPCs lives outside of quest giving. All the major quest-givers were still stationary, but secondary ones and non-quest related NPCs would move around from place to place, comment on their day, and participate in different activities which was a real new thing to see in a major MMO in early 2004.
Open World:
Open world or 'sandbox' games are probably closer to Sui Generis' alley. As long as you ignore the main plot, it seems, which tends to be fairly short and tacked on in the end.
Elder Scrolls Morrowind -> Skyrim
One word: Exploration. Morrowind through Skyrim were all just huge treasure troves of places to oggle at. A million things to do, with a million ways to do them. Most people are pretty familiar with these titles, but the major themes, a little mystery, and the hiding of history in in-game books are all great features. Not to mention that as best they could without preventing quests, NPCs were almost all killable. I especially liked in Morrowind where you could choose to kill someone important, but were warned that the plot would not be completable if you went through with it. As with almost all Bethesda games, the Elder Scrolls (and Fallout below) had characters with completely dynamic schedules. They got up, did their daily routine, left the house, etc. It was so lifelike it was hard to think of it as a mechanic at that point because it was just done so well and naturally.
Fallout: New Vegas
Factions, factions, factions. New Vegas was the great Crowd Pleaser. You had to make choices that impacted a huge number of other characters by supporting one faction or another. Half the world might go after you if you couldn't stay neutral, which not only encouraged huge re-playability, but put in great moral dilemmas for supporting your 'side' or the right side, as they often switched from scenario to scenario. The characters were also compelling, and much like Sui Generis, no one's special: if your companion dies, they die for good (granted this is also true for Skyrim, but not every character).
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