The Facts
1.) The G-man has a somewhat large connection with black mesa, and was seen re-arming the bomb that led to his destruction.
2.) The Vortigaunts have knowledge of the G-man and keep him at bay from Gordon and alex through episodes one and two. It appears that He could only contact gordon through his dream-sequenzce while they were occupied.
3.) The G-man rescued Alyx Vance, Gordon Freeman and Adrian Shepard from black mesa before the destruction of the facility. Though Adrian has not come up again in the storyline so far.
4.) Eli vance hinted to knowing a lot more about the G-man than we know, and was killed by the advisors before Alyx and Gordon Set off for the borealis, which was either predicted or made to happen by the G-man
5.)The G-man appears in a lot of TV-screens and unreachable areas throughout the game, and by the time Gordon gets there, there is no sign of him.
My thoughts
There are a lot of theories going around that the G-man can travel in time, and has done so because he is the future Gordon freeman and is trying to steer him into certain events which would otherwise save his life or something similar. But why the sudden change in character? Where did the powers come from? The ability to contain Freeman and Adrian in statis for two years. The suit. And why be so secrative? Why not just tell himself the truth? And of course, the biggest argument against the Gordon is the G-man argument- Gordon is a MUTE. He cannot speak. This has never really been confirmed as far as i'm aware, but if he could speak, he probably would have talked to Breen, Isaac, Eli, and Alyx all the times in the cutscenes. And all those characters act as if they don't expect a
response from him.
To Opposing force. G-man is seen aiding and hiltering shepard at certain points in the game. My theory as to why he does both of these is that he wishes to test shepard. The G-man aids shepard when it is impossible for him to go on or in times where he faces certain death, and hilters him when things seem too easy for him. That was what G-man was doing in Black Mesa. Testing Gordon and Testing Adrian. He delivered the sample and he knew the resonance cascade would happen. We know this Because Eli confirms it in episode 2. He said the same words he told Alyx to tell his father before his death. "Prepare for unforseen consequences."
But what If Freeman and Shepard failed? Even if the G-man destroyed Black Mesa, that would not stop the invasion from Xen. So maybe the G-Man could control the Nihilanth all along. He obviously had stakes in the "Test" and it has been proven that the Vortigaunts could interact with him. But then again, i'm contradicting myself. If he could control the Nihilanth, then why couldn't he prevent the Vortigaunts from stopping him putting Freeman and Alyx Back into Statis? (Assuming that was what he was supposed to do. If he could control the overmind of the Alien slaves, surely he could control the slaves, no? I think the vortigaunts are extremely powerful, and the green collars they wore not only signified that they were slaves, but restricted their powers. Note the Vortigaunt being used as a slave to the right of the station at the start of Half life 2

This Vortigaunt is wearing similar collars, but wouldn't the combine be a fool to try to inslave it if it could just fight back? No, because its powers were restricted. A Vortigaunts true powers are similar to the G-man's.
Half life 2
Two years later, and the combine have taken over the planet, and suppressed the reproduction cycle, allying with Wallace Breen, the so-called spokesman for the human race. The combine tried to enslave the human race, unbeknownst to Breen because he was drunk with power, or too much of a coward to object to what the combine were doing. The humans freed the Vortigaunts and City 17 later turned into a battlezone.
The G-man often speaks of his "Employers", and at one point says he has agreed to abide by certain "restrictions" this probably refers to how he can not interfere with the situation of the combine, which is why he needed Freeman, and Adrian probably as a backup. The Perculiar thing is why the G-man tried to contain Freeman again after he had killed Breen. My guess is that the portal storm was not how the G-man predicted Gordon to create, and consequently, had to detain him and see how time played out.
Episode 2
At the end of episode 2, everything went exactly how the G-man planned. Eli died without letting Gordon know what he knew about the G-Man, forever maintaining the secrecy he so desperately needs. The reason is unclear. But the means of how he did it are so contradictory to my theory. he managed to take control of an advisor, and use it against, Eli, which is in direct defiance of the restrictions his superiors made him abide by. Perhaps the G-man defied them, because the Vortigaunt Barrier that they had set up would also prevent his superiors from knowing his actions.
The Borealis
The G-man saw the Borealis as an oppertunity- a last resort against the combine, to use its immense power to destroy the combine race. And that gave him more reason to kill Eli. Eli was trying to convince Gordon to destroy the Borealis, and with him out of the way, Isaac would surely convince the two to use it against the combine.
My conclusion is this: The G-man was testing Freeman and Shepard with the events of Half life 1 and Opposing Force, in hopes to gain resistance against the upcoming war against the combine in which his Superiors had forseen.
~Stryder.