I voted Eberron. I enjoy the setting for many reasons, but ultimately, they revolve around the fact that they make the setting more 'real' than others I have come across (and enjoyed, for their own good points, though not as much as Eberron). The fantasy elements of D&D are given an actual place in the world, and it that the current situation of magic and monsters in the world has actually grown organically.
First, magic. Eberron is not a high-level magic world; instead, the setting focuses on everyday life, and how magic affects the common people. Mages are not holed up in their towers. Their main effect on the economy and ecology is not to attract other adventurers as either allies or enemies: they are integrated into society. They are technicians, researcher, businessmen. The magewright npc class exemplifies this, as do the Dragonmarked Houses.
The Lightning Rail is putting some people off the setting, and that is a reaction I can understand. But this mass-transport system feels, at the end of the day, more believable than a flying carpet. It makes money for Orien, and acknowledges the fact that economy rules many cultures. It has its own history, and, at the risk of repeating myself, it has a place in the world. It represents the unity of the Kingdom of Galifar, shattered in the Last War - many of the lines are broken now. It simply fits in, and (besides some attempts to fit the umpteenth elf or dwarf subrace into the setting, but that does not happen in the ECS), hardly anything feels imposed in Eberron.
Likewise, as has already been said, monsters have their place in the world. They are not simply monsters. If they are at war with another race, it is because of their own reasons - economy, ideals, territory, politics - not because their respective creators don't like each other. Monsters have motives, personalities and culture. The orcs and goblins are not simply there to be killed by adventurers. Likewise, races are not simply good or evil. Eberron's drow, as an example, don't kill the visitors from Khorvaire because they hate them, but because they encroach on their territory, risk disturbing ancient curses out of sheer greed, and are themselves not the nicest people around: Stormreach was founded by pirates, after all.
Which leads to the alignment issue. That too is a major point in Eberron's favour in my book. There is no looking at anything short of an embodiment of evil and saying, without a doubt, "that's evil!" I've mentioned drow. The same goes for dragons, but also religions. I also like that a good person in Eberron can still do evil, and that destroying a villain could have even worse consequences. Queen Aurala and King Kaius III are examples for this: the good, caring Queen who may not want war, but believes it will happen so she had best face it, and the evil king who wants peace but is ready to do whatever it takes to get his people to stay on that path. Riedra is another example: it's lords do not even intend anything good, but destroying them would be a catastrophe as far as the commoners are concerned - and even the vile Quori are not evil for evil's sake, but try to survive themselves.
The same holds true for religion. I do not like it when gods walk the world. That is purely a matter of personal opinion, as everything else is, of course, but I'd rather play a cleric who believes in his god than one who knows him. To me, the former actually has belief, the latter is simply following a liege-lord who happens to have some supernatural powers. This also means that a priest of a good god can be evil, as long as he can justify/fool himself, but not beyond that. A priest of the Silver Flame who comes to realise and relish his evil cannot draw on the Flame any more (he may go over to the Shadow in the Flame), but as long as he truly believes, he is safe. That too creates a lot of roleplaying opportunities.
Eberron is a setting where I find it much easier to immerse myself. Because elements have their actual place in the world, because there is information on everyday, non-adventuring life, it feels easier to actually role-play. Eberron even managed to balance its feats against this: dragonmarks are not very powerful, taken purely on their own. But the roleplaying opportunities and the actual meaning behind having a dragonmark, and with it a place in the world, make more than up for that.
There are many other elements I could manage. As I like the way Eberron seeks to have everything fit into the world without having elements float around as if they were grafted on, I adore the planar system. Eberron has planes that are not easy to reach... but Lamannia affects every farmer on the material world every year. Eberron has psionics, and fits them in, too with both the Quori and the Daelkyr. Eberron makes its dragons intelligent, civilised creatures rather than predators: again, they fit the world better. And so, at the end of a long post, I come back to where I started: Eberron just feels much more logical, much less suspension-of-disbelief involving than other worlds.
A word on the two other contestants.
I admit I have not tried Rise of the Runelords. As has been pointed out, it is primarily an adventure. As such, it does not appeal to me. I really enjoy Eberron beyond the ECS, but even there I have not bought any of the adventures. I prefer setting information than being guided through a single story, however complex it is. Naturally, that is again a matter of taste: it is not because there is a flaw of Rise of the Runelords that I did not vote for it, it is simply that I do not enjoy reading or playing adventure-paths all that much.
As regards Unearthed Arcana: I enjoy the book. I use many of its elements. I like most of the variant classes, the paragon levels, even the bloodlines. I use spell-points, flaws (though I prefer the dragon magazine ones, UA introduced them into 3.5), traits, spell-touched feats and even gestalt rules. But there are equally many elements that I do not use. Ultimately, it also comes down to the fact that Unearthed Arcana is a crunch book. It has very useful material in there, but it is not as interesting or immersive as Eberron. It is also not what keeps my interested in D&D: that again is Eberron (which is also the only 4e books I consider buying, and the reason I might pay for the online magazines), especially now the setting will not advance in its time-line.
So my choice has to be Eberron.
