The Yogg-Saron encounter in Ulduar consists of three phases and has some similarities with the C'Thun encounter in Temple of Ahn'Qiraj.

The encounter starts when you simply step into the room with Sara. Once started you have 15 minutes to beat Yogg-Saron, after 15 minutes Yogg-Saron will hard enrage and one-shot everyone in the raid.

Phase One: Sara's guardians

From the clouds in the room Guardians of Yogg-Saron will spawn at an increasing rate as phase wears on, these have to be picked up by the tanks and DPSed down. To end phase one 9 or 10 Guardians of Yogg-Saron have to be killed next to Sara.

When players touch the clouds in the room a Guardian of Yogg-Saron will spawn from that cloud (pets and totems do not trigger additional spawns), this can lead to a raid wipe. The clouds always follow the same path and can move faster then you think. Because of the orbiting behaviour of these clouds the outer edges of the room are less frequently visited by these clouds making it easier to setup the raid there. A general rule in this part of the encounter is to stop all that you are doing when a cloud comes close and move away from it, 3 seconds DPS / Healing lost in this encounter doesn't matter so much as an extra Guardian of Yogg-Saron.

While they are active the Guardians of Yogg-Saron can cast two spells, Dark Volley which can and should be interrupted and Dominate Mind which can and should be dispelled as soon as possible, as an undispelled Dominate Mind can lead to a raid wipe when the controlled people run through clouds.

Upon death the Guardians of Yogg-Saron will cast Shadow Nova dealing massive AoE damage and therefore no one but the tank (and Sara) should be near it when it dies.

There are several ways to deal with the Guardians of Yogg-Saron in this phase, and raid composition matters a lot when choosing the method of dealing with the Guardians of Yogg-Saron. A melee heavy raid might want to DPS down the Guardians of Yogg-Saron away from Sara and then drag the Guardians of Yogg-Saron down to Sara on Low HP so that the ranged DPS can finish it off.
While a ranged heavy raid might opt for DPSing down the Guardians of Yogg-Saron near Sara to speed up the killing process.

Each method has it pros and cons in terms of speed and cloud dodging.

A highly effective method of speeding the encounter up is to touch a cloud at the start of the phase to spawn an extra Guardian of Yogg-Saron as the spawn rate at this point in time it's so high that it can't be dealt with.

In the mean time Sara will be casting her spells throughout phase one, however these are a minor part of the phase.

Phase Two: Tentacles and the Brain

When phase two starts any remaining Guardians of Yogg-Saron from phase one should be killed at a save distance from the raid as soon as possible. They will still cast all their spells from phase one.

Phase two consists of two areas, outside and the brain "room". During the phase Yogg-Saron will open portals to the brain "room". After Yogg-Saron has opened portals four times the spawn rate of the tentacles outside will increase possibly leading to a raid wipe. No more then 3 portal phases should be used to get to phase three.

During phase two three types of tentacles will spawn outside the brain "room":

And inside the brain "room" another type of tentacle will spawn:

Phase two ends when the Brain of Yogg-Saron hits 30%. This removes the invulnerability from Yogg-Saron's main body.

Outside: Tentacle party

Once all the remaining Guardians of Yogg-Saron of Yogg-Saron have being dealt with, the ranged DPS should focus on the Crusher Tentacles while the melee DPS focuses on the Corruptor Tentacles. It is possible for the melee DPS to help out on the Crusher Tentacles, however much like the Snaplashers in the Freya encounter, the Crusher Tentacles get a stacking buff which increases their melee speed and damage.
During the phase random people will get picked up by a Constrictor Tentacle which will squeeze slowly to death. While in a Constrictor Tentacle casters can still DPS the tentacle and should do so. Also the other players need to free the caught players quickly. To make freeing caught players easier the raid should try and stay together.
Corruptor Tentacles will cast numerous spells at players which can and should all be dispelled by various classes. Corruptor Tentacles do not melee can and should be interrupted and stunned while killed by the melee DPS.
Sara will hover above Yogg-Saron's main body casting various spells:

Brain Linked players will get a linking beam between them which is red or yellow. When the beam is red the players are too far apart and both players will take damage and lose sanity. As soon as the beam is yellow the players are close enough together. Upon entering a portal to the brain "room" the brain link is severed without additional effects.
When Sara casts Death Ray small green beams will appear, and after a few seconds these will become bigger, begin to move around, and start doing massive damage. The beams need to be avoided.
60 seconds into phase 2, and then 20 seconds after each brain phase, Yogg-Saron will open portals into the brain "room" allowing players to enter (4 on normal, 10 on heroic). When Yogg-Saron opens the portals he will yell: "MADNESS WILL CONSUME YOU!"
Assign good DPS and one healer to take the portals. Players assigned to take portals should pay extra attention to their sanity level and use the Sanity Wells (Freya) to recover sanity before entering the portal.
Because of the Crusher Tentacles outside mostly melee DPS should enter the portals so that ranged DPS can focus on these tentacles.

Inside: Illusions, Madness and a Brain

Once inside Yogg-Saron's mind you have 60 seconds to get out before you become utter insane by the Induce Madness cast.
You will see one of three random illusions along with some disguised Influence Tentacles and laughing skulls floating around the room. The skulls cast Lunatic Gaze so you must strafe around the room with your back to the skulls at all times. When you look at a skull you'll see a purple beam between it and your character.
The illusion will shatter once you kill all the Influence Tentacles in the room.
Once the illusion shatters the DPS inside can enter the brain "room" and DPS the brain. Also in the brain "room" there is a portal back out. When there is 10 to 5 seconds left on the Induce Madness cast timer the players inside need to start getting out of the brain "room".
The players outside the brain "room" should see all the tentacles become stunned when the illusion shatters. Also no new tentacles will spawn, and Sara stops casting her spells. This gives the players outside time to catch up on tentacles.

Phase Three: The Head of the Beast

When phase three starts all tentacles left over from phase two will remain active. Any remaining Crusher Tentacle should be dealt with. As long is there only a limited of Corruptor Tentacles up these can be safely ignored as long as the debuffs are dispelled.

Phase three will end when Yogg-Saron dies. Yogg-Saron has no aggro list and is unable to move.

At the start of the phase the raid needs to choose a spot and bunch up there. The best spots are obviously near the green pillars if Freya is helping so that players can restore sanity. All healers should be facing away from Yogg-Saron at all times. The caster camp is best located about 20 yards away from the melee camp. Melee DPS can get knockbacked by Yogg-Saron when attacking him.

During this phase Yogg-Saron will cast Lunatic Gaze which will be displayed as purple beams between Yogg-Saron and the players facing him. Only when all players stop facing Yogg-Saron will the cast be broken, this is the main reason why healers need to look away at all time.

Yogg-Saron will also spawn Immortal Guardians. These Immortal Guardians have to be picked up by the tanks and DPSed down fast. As they spawn they'll hit a well geared tank for 25k, but their damage is dependant on their HP, the lower they get the softer they start hitting. If Thorim is helping then the Immortal Guardians can be killed otherwise they need to be tanked throughout phase three. Yogg-Saron will cast Empowering Shadows to heal the Immortal Guardians.

Phase three is mostly a burn phase, where you have to kill Yogg-Saron quickly. Caster DPS should focus solely on Yogg-Saron and help out on the Immortal Guardians only when they are swarming the melee camp. And the melee should focus on the Immortal Guardians and only DPS Yogg-Saron when no Immortal Guardian is being tanked.

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