From my gun-knowing fiance: The classic American gun is the Colt .45, but it's not exactly subtle. The other thing you could use is the H&K Mk.23 USP SOCOM. It's the pistol that's issued to everyone who's special services for the military.... Navy SEALs, Green Berets, etc. Woodstock cops carry Glocks, but Cobb County cops carry Barrettas.
Secret agent is really to vague. Many agents would carry no weapon whatsoever; they are information conduits only, trained to be inconspicuous. Possession of a weapon would compromise their cover. If you are talking about a James Bond type of agent in the CIA or some ultra-secret agency, the "daily gun" would have to be a small flat hangun that wouldn't show a bulge. Such a weapo would likely have limited stopping power, unless the agent is extremely accurate with his or her targeting. Other situations might require a more serious weapon. If he has to travel frequently, he will not want to draw attention at security checkpoints. A special weapon made of a non-metallic composite might be necessary, and te ammunition would have to be equally specialized. You won;t find it in any of the gun manufacturers' catalogs.
Colt .45 are no longer in general use by the DoD as far as I know, if we use them at all. I know some law enforcement agencies still use them but that's not really spy stuff. Besides, everyone knows the Colt Single Action Army is the greatest gun ever made. "Secret Agent" is indeed vague, as different branches of the DoD have different standard issue weapons for their purposes. Some agencies have no standardization, and agents simply pick whatever works best for them. In the US Glocks are relatively popular as personal side arms. Walter PPK's are classic spy guns though I don't know if they're actually in use by spies XD. You could probably give the spy anything realistic that fits their purpose and probably get away with it. Whatever you do, don't go Revolver and don't go into the hand cannons. Revolvers are impractical for secret agent stuff because of their bulk and reload. Hand Cannons as I've dubbed them like the the Desert Eagle, though very cool, are probably the most impractical weapons on the planet. A 50 caliber pistol is overkill to the extreme and the recoil makes them seem kind of worthless to me.
Back in the 60's, some spec ops used .22s with a silencer for some anti-personnel missions. Traditional snipers made too much noise and the risk of the shooter's capture was high when operating deep in enemy territory. If stealth, both before and after the kill was paramount, silenced .22s were the best choice. They were also very deadly when used right, untraceable and inexpensive -- hence, disposable. edit: Yes, silencers violated certain "rules" of war but they were used anyway by the US and others . . . still are.
