Jacob has been in practically every episode of the show, including the pilot by Chris Hollander

In the first episode, a man on the beach wiggles his toes, stands up, and takes a few steps. At the time, we didn’t really take note of anything special about this… it would take a few episodes before we realize that that man, John Locke, was apparently paralyzed, and wheelchair bound, for the better part of his life before flight 815.

During the first episode, Locke stood out as somehow different. He sits calmly, looking out at the ocean, across the sea, while chaos swirls around him. Later on, when a sudden downpour comes over the beach, Locke just sits and enjoys the rain, while everyone else runs for cover. He gives Kate a weird “orange” smile.

In the second part of the first episode, Locke and Walt have a great scene. Locke introduces Walt to backgammon. He explains that the game is over two thousand years old, and that it was originally played with bones as dice. He then explains that the game has two sides- one light, one dark… and asks Walt if he wants to know a secret.

Everything we needed to know was laid out before us, right then and there, in the pilot.

in the next few episodes, we learn more about John. Locke told Walt that a miracle happened to him. Locke seems to know an incredible amount about the island wildlife. We soon learned a bit about John Locke’s past, and the circumstances that led to him being on flight 815.

While out hunting boar with Kate and Michael, Locke is “confronted” by the Smoke Monster. We see, through the Smoke Monster’s eyes, that Locke and the monster look directly at each other. Later on, Michael asks Locke if he got a good look at the monster, and John lies- he says, flatly, “No”.

Locke brings the survivors fresh boar. When Jack almost dies by falling off of a cliff (Led there by an image of his father, who was most likely the Man in Black), Locke is there to save him. Locke encourages Jack to be a leader, and is understanding when Jack explains that he was chasing after something. The next few lines are critical, so it’s easier for me to just copy it here:

LOCKE: I'm an ordinary man, Jack, meat and potatoes, I live in the real world. I'm not a big believer in magic. But this place is different. It's special. The others don't want to talk about it because it scares them. But we all know it. We all feel it. Is your white rabbit a hallucination? Probably. But what if everything that happened here, happened for a reason? What if this person that you're chasing is really here?

JACK: That's impossible.

LOCKE: Even if it is, let's say it's not.

JACK: Then what happens when I catch him?

LOCKE: I don't know. But I've looked into the eye of this island. And what I saw was beautiful.

We now know where the heart of the island is. We now know exactly who has seen it, and who hasn’t. The heart of the island is the cave of light. Jacob’s cave. Jacob has seen it. Jacob guards it. From the moment the plane crashed until the moment John Locke was killed by Ben, the character that we thought was Locke was actually Jacob. John Locke died in the plane crash. Jacob was inhabiting his body the entire time.

With this in mind, all of ‘John Locke's actions suddenly make more sense. Jacob brought all of the candidates to the island. Once they were there, as Locke, he tried to show each of them that they had a purpose- that “the island had a purpose” for them. He helped Charlie with his addiction. He helped Jack be a leader. He tried to help Michael and Walt’s relationship. He tried to help Boone become more independent from Shannon. On and on, down the list, he helped each of the candidates.

In the second to last episode, Jacob explains that he brought the candidates to the island to replace him. Above all else, John Locke’s most important mission was keeping the candidates on the island- nothing was more important to him, because he was Jacob. Throughout the entire show, as early as season one, Locke sabotages every attempt the candidates make to get off the island. He starts by knocking out Sayid, spoiling the plan to use the radio to transmit a signal. Locke destroys the sub that the others provided for Jack to leave the island. Locke kills Naomi when she’s about to communicate with the freighter.

Jacob also explains that he wanted the candidates to have the one thing he never had: a choice. In Season 1 Episode 7, the Moth, Locke has this exchange with Charlie:

LOCKE: I think you're a lot stronger than you know, Charlie. And I'm going to prove it to you. I'll let you ask me for your drugs three times. The third time, I'm going to give them to you. Now, just so we're clear, this is one.

CHARLIE: Why? Why? Why are you doing this? To torture me? Just get rid of them and have done with it?

LOCKE: If I did that you wouldn't have a choice, Charlie. And having choices, making decisions based on more than instinct, is the only thing that separates you from him [indicating the boar].

Locke, Jacob, gives Charlie a choice. Jacob also explains that the common thread amongst the candidates is that they were all “Lost” in their lives- they were searching for purpose. They needed the Island as much as the Island needed them. When answering Hurley’s Census questions, Locke answers:

HURLEY: Cool. And, reason for travel? The reason you were in Australia?

LOCKE: I was looking for something.

HURLEY: Looking, uh-huh. So, did you find it?

LOCKE: No. It found me. Anything else?

John Locke was lost in life. He was looking for purpose. He died in the plane crash, and Jacob, purpose, found him.

In the middle of the third season, Locke asks Eko what he saw when the smoke monster “inspected” Eko:

LOCKE: So, what exactly did you see back there? I saw it once, you know.

EKO: And what did you see?

LOCKE: I saw a very bright light. It was beautiful.

EKO: That is not what I saw.

Once again, ‘Locke’ describes a beautiful, bright light. The light that Jacob is guarding.

In season 3, Locke/Jacob takes up a position as leader of the others. Ben explains that there is a “magic” room, that can “produce” anything that Ben wants. Ben produces Anthony Cooper- John Locke’s father- and explains that Locke must kill his father in order to be accepted as their leader. It’s very likely that the ‘produced’ Anthony Cooper was, actually, the smoke monster- Jacob’s Brother. This is why Locke/Jacob couldn’t kill Anthony Cooper/Mib. Once Locke/Jacob proves himself to Ben and the Others, he demands that Ben brings him to ‘Jacob’s Cabin’. He was doing this because MiB has been masquerading as Jacob to the Others, and Jacob wanted to confront him!

In seasons 4 and 5, we see that candidates actually succeed in getting off the island, despite everything that Locke/Jacob did to keep them from leaving. Locke then leaves the island as well, by “correcting” the frozen donkey wheel machine. Locke/Jacob was essentially chasing after the candidates, trying to get them back to the island.

Locke/Jacob ultimately succeeds in his mission, but it costs him his life- or, more specifically, his “host” body, in the form of Locke, at the hands of Ben (btw, I suspect Locke/Jacob would have never been able to kill himself). This, of course, set the wheels in motion for most of the events of season 6- his death led Jack to rally the troops and return to the island, with Locke’s corpse… which then allowed the MiB to take up residence within Locke, which then allowed (f)Locke/MiB to tell past Richard to tell previously Jacob/Locke that he had to die, and to bring the candidates to Eloise Hawking. Also, once Locke/Jacob was killed by Ben, Jacob returned to his pre-flight 815, drawstring-pants+fluffy shirt existence.

So, its late, and I've been rambling for quite a while. Here are the cliff notes:

Since the crash of flight 815, every single time we’ve seen the character John Locke on the screen, we’ve actually been seeing either Jacob or the MiB using John Locke’s body.
From the minute the flight crashed until the moment that Ben strangled him, Jacob was trying to get the candidates to understand their destiny, and choose to stay and protect the island.
MiB has been orchestrating the destruction of the island for hundreds or thousands of years. Dharma, Whidmore, and Hawkings are probably all part of his plan.
Ben has killed Jacob twice. Once by strangling Locke, and once by stabbing him in the heart.