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In TES: Skyrim, there are numerous Dwemer ruins located in various parts of the region, but the Dwemer themselves are mysteriously absent. What happened to them?
I seem to remember reading or hearing something in-game about them reaching too far in their ambitions and being punished by the gods, but I'm sure that there is a better answer than that.
So what actually happened to the Dwemer?
No one knows what happened to the Dwemer, it's one of the biggest mysteries of the Elder Scrolls universe. If you play through the game Morrowind, you will learn just about everything we know about the Dwemer and what happened to them. The rest you can find in scattered in-game books.
Basically, back in the First Era (~3500ish years ago) there were no Dunmer. At that time, they were still Chimer, and shared the Morrowind area with a second race of Elves, the Dwemer. The Dwemer were about as close as the Elder Scrolls universe comes to having dwarves: they lived underground, and were very mechanically inclined. They were very good at blending magic and mechanics together, to the point where many of the Dunmer myths revolve around the Daedra (the Chimer's gods) being pissed off at the Dwemer for blasphemy.
At some point, one of the Dwemer found the "Heart of Lorkhan" (the Aedra who's body supposedly became the physical manifestation of Nirn). Whatever it was, the object was immensely powerful, and one of the Dwemer architects -- Kagrenac -- devised a set of tools that he claimed would let him tap into the power. Among other things, he planned to use it to power a giant golem (Numidium), and to make himself immortal.
This is basically the setup for the modern Dunmer society, and Morrowind in particular: a group of Chimer, led by the people who would go on to become the Tribunal, attacked Kagrenac's stronghold beneath what is now Red Mountain. During that battle, something unexplained happened and the entire Dwemer race vanished. At the same time, the Chimer were transformed into the Dunmer, and many of them shifted from worshipping the Daedra to worshipping the Tribunal.
Details of exactly what happened during that Battle are sketchy and contradictory (not surprising, given how long ago it happened). There are several theories, depending on which group you ask:
One interesting footnote, though: the Dwemer did not all disappear. In particular, you meet one in Morrowind, though he's in bad shape; he's suffering from Corprus, a "disease" that plays a key role in the end-game of Morrowind. Much of his body has been replaced by one of the Dwemer's mechanical spiders. Unfortunately, he has no idea what happened to his people, any more than anyone else.
I found a site that talks briefly about it (http://elderscrolls.wikia.com/wiki/Dwemer See:The aftermath of the Battle of Red Mountain).
According to legend, after Lorkhan tricked or convinced the Aedra to create the mortal realm, they tore out his divine heart and threw it down to Nirn, to be hidden forever. Tensions had begun to flare between the Chimer and Dwemer once again when Kagrenac—the Chief Tonal Architect of the Dwemer—prompted the discovery of a mythological artifact known as the Heart of Lorkhan, deep within the mountain. When the Chimer heard of this, they believed the Dwemer were mocking their cultural beliefs; as a result, a second Battle of Red Mountain erupted in 1E 700. Kagrenac devised a set of tools, Sunder, Keening, and Wraithguard, to manipulate the Heart to instill divinity in his people, in order to make them immortal. However, the spell seems to have backfired, causing all known Dwemer to vanish in a manner similar to a Dragon Break.
So, the spell to "manipulate the Heart to instill divinity" into the Dwemer people backfired and destroyed the race.
"I think Kagrenac might have succeeded in granting our race eternal life, with unforeseen consequences -- such as wholesale displacement to an Outer Realm. Or he may have erred, and utterly destroyed our race." ―Yagrum Bagarn
Just to add to the other answers, there are conflicting accounts of what actually happened. The Tribunal Temple has an agenda to further itself by legitimizing the deification of the Tribunal/Almsivi Almalexia, Sotha Sil and Vivec. There is another faction of the Temple, called the Dissident Priests, whose teachings align with that of the Ashlanders.
Each of these two factions have published books (in universe) that reference the events at Red Mountain. The Tribunal uses it's power to suppress the teachings of the Dissident Priests.
Excerpt from Progress of Truth by the Dissident Priests
Ashlander tradition does not place the Tribunal at Red Mountain, and holds that the Dwemer destroyed themselves, rather than that Nerevar destroyed them. Ashlander tradition further holds that Nerevar left Dagoth Ur guarding the profane secrets of Red Mountain while Nerevar went to confer with the Grand Council [i.e., the Tribunal], that Nerevar died at the conference [not of his wounds, according to the Ashlanders, but from treachery], and that subsequently the Tribunal confronted a defiant Dagoth Ur within Red Mountain, then drove Dagoth Ur beneath Red Mountain when he would not yield to their will.
The Tribunal Temple's official account is recorded in Nerevar at Red Mountain.
And so the Chimer and Dwemer went to war. The Dwemer were well-defended by their fortress at Red Mountain, but the bravery and cleverness of Nerevar's queen and generals drew most of Dumac's armies out into the field and kept them there, so that Nerevar and Dagoth-Ur could make their way into the Heart Chamber by secret means. There, Nerevar met Dumac and the Dwarf King and they both fell from grievous wounds. Dagoth-Ur slew Kagrenac and took the tools the Dwemer used to tap the power of the Heart. He went to his dying lord Nerevar and asked him what to do with these tools. And Nerevar summoned Azura again, and she showed them how to use the tools to separate the power of the Heart from the Dwemer people. And on the fields, the Tribunal and their armies watched as the Dwemer turned into dust all around them as their stolen immortality was taken away.
The Nerevarine also has a conversation with Vivec where he references the Dwemer, and the aforementioned two books.
"In my library, I have made available two conflicting accounts of the events of Red Mountain, my own true account, and another false account common among the Ashlanders and preserved in the Apographa. I don't care whether you believe my account or not. I leave it up to you to judge which is true."
"The sin of the Dwemer was the creation of a new god from the substance of a dead god, Lorkhan. That is also the sin for which we would destroy Dagoth Ur. I hesitate to call it 'sin'. More properly, call it 'destructive evil'. The sin of the Tribunal, however, is in the breaking of an oath to Azura to forebear from tapping the Heart with Kagrenac's tools, and in the folly of seeking to become gods. Breaking the oath was evil. Becoming gods was folly. If we sinned, we have paid the price."
"I have no idea what happened to the Dwemer. I have no sense of them in the timeless divine world outside of mortal time. And, in fact, if I did believe they existed, I would be in no hurry to make contact with them. They may, with some justice, hold the Dunmer race responsible for their fate. My intuition is that they are gone forever -- and that is perfectly fine with me."
Doing some reading, I found another interesting reference in The Thirty-Six Lessons of Vivec, Sermon Thirty-Six
Dwemeri high priest Kagrenac then revealed that which he had built in the image of Vivec. It was a walking star, which burnt the armies of the Triune and destroyed the heartland of Veloth, creating the Inner Sea.
Each of the aspects of the ALMSIVI then rose up together, combining as one, and showed the world the sixth path. Ayem took from the star its fire, Seht took from it its mystery, and Vehk took from it its feet, which had been constructed before the gift of Molag Bal and destroyed in the manner of truth: by a great hammering. When the soul of the Dwemer could walk no more, they were removed from this world.
Resdaynia was no more. It had been redeemed of all the iniquities of the foolish. The ALMSIVI drew nets from the Beginning Place and captured the ash of Red Mountain, which they knew was the Blight of the Dwemer and that would serve only to infect the whole of the middle world, and ate it. ALTADOON DUNMERI!
Lorkhan is the son of Sithis, the dread father, the void.
The Dwemer tinkered with the heart of Lorkhan, and then were immediately sent into the void, instantaneously, all in all, with the exception of one Dwemer who did not exist within the plane susceptible to Sithis' influence at the time.
This is the easiest explanation. I don't know why it's so speculated.
There is a theory about the Dwemer being tied to Kagranac's gigantic Automaton since if you do a certain mission a guy's shade is attached to you as a conjuration spell so the theory is that the same thing happened but it had the Dwemer attached to the gigantic automaton as a shade to it might be possible for it to summon them all back into existence but not in a proper form due to them being shades.
My answer is they found a way to enter the Elder Scrolls you could say. If they can make a way to read a scroll what makes you think they can't enter them. That would explain why nobody can recall the date they vanished. If you think about it how could nobody know when they vanished without the help of the scrolls.
