Apologies for the lack of posts, RL has been a demanding (but rewarding) mistress of late.
On to the topic. I've played a lot of MMOs over the years, and it seems that all too often nice features are buried in obscure or mediocre products. In no particular order, these are my personal top three.
1. Procedural Quest Generators (Anarchy Online): SWG had something similar, but no MMO that I have tried had a random quest generator as deep as the one used in Anarchy Online. There were a series of sliders so that you could adjust the missions for your class, playstyle, and party size. To give one example, by adjusting the sliders you could generate missions that were combat heavy "break down the door and shoot everyone that moves" missions or missions where you could win by stealthing past everyone and stealing an item. Once you had the mission parameters set the way that you liked them, you could randomly generate missions over and over until you got one with a quest reward that was useful to you.
The brilliance of the system was that it provided unlimited content that players themselves balanced to their tastes, rather than forcing some designer to guess what the players will want. The missions did get repetitive eventually, it's nothing you'd want to hinge your MMO on. However, adding that sort of system to a game that already has a deep scripted questing environment would definitely add a ton of value to an MMO, and with a lot less developer overhead than creating new zones or quest hubs. When I played Anarchy Online I got a solid month of entertainment out the mission generator.
2. Flexible yet Simple Crafting (EQOA): It seems that in most MMOs, either your crafting is limited to predefined recipes or the crafting system is way way too deep to be entertaining for casual players. The sole exception that I am aware of is Everquest Online Adventures. Crafted items had base stats like AC or DPS. The other properties of an item were determined by the gems you included while crafting an item. Gems could add to any base stats, and could also add properties like offensive procs on weapons and defensive procs on armor. Instead of hunting around for a recipe that made a good item for a given character build, you simply designed it. Want a full set of Intelligence plate-mail for some insane reason? Just make it. Remarkably, the system for crafting was actually no more difficult to figure out than something like WoW or LoTRO. Assemble ingredients and hit a button.
3. Diablo Style Endgame (Phantasy Star Online): In Phantasy Star Online, once you reached a certain level you gained access to new dungeons where mobs could drop the highest level loot. Admittedly they weren't really new areas, but the same areas that you had been adventuring in with new monsters that behaved differently and had different resistances. However, either solo or in four man parties, the eight "final dungeons" were extremely addictive to play through. Loot was completely randomized, and the best items were fantastically rare (1% or less drop rates rare).
At first gear drops that were enormous upgrades would come quickly. However, once your gear hit a certain threshold the odds of getting an upgrade on any given run was pretty low. Despite this, PSO kept me playing in the "endgame" longer than almost any other MMO I've tried. I literally put in hundreds of hours into the final dungeon tier, and to this day I still play offline occasionally. The "maybe I'll get something this time!" mechanic is extremely addictive.
What I really liked was that the endgame supported both casual and hardcore playstyles. It rewarded casual players by being accessible solo. However, it also rewarded the super-hardcore because they were far more likely to have stumbled across the best gear. I find it a bit mystifying that Diablo/ Rogue style dungeon mechanics don't appear in more MMOs (Dungeon Runners excepted).