Depends on the quality of the weaponry on offer (see Yatzhee's recent XP column) but if it's all good, the sniper rifle from distance, shotgun for up close. I prefer precision on which score the sniper rifle speaks for itself- it's that godlike sense of deciding your enemy's fate before they are even aware of it. Combining the sniper rifle with Adrenalin Rush in ME2 was near perfect, it turned the Viper and Widow rifles into viable firefight weapons as well as stealth/distance options. It almost felt unfair
Shotguns aren't always done right- the shotties in both ME2* and Gears were pretty unsatisfying, but the shotgun in Half Life 2 was a damn near perfect blend of force and a thunderous kick. The wide blast zone might make it seem a blunt instrument but unlike an assault rifle where you can spray until you hit, if you mistime the shot or spin too far during close in combat, there is always that extra second of exposure as you reload. The tradeoff is the feeling that you're kicking the enemy in the head with a thousand tiny pellets of hot death and watching large chunks of their health disappear at a time.
*I opted for the unusually satisfying Hand Cannon instead. One of the rare handguns that was a pleasure to use, sort of like the magnum in RE4 except with a decent replenishable ammo supply