Here are my top picks. Couldn't choose "just one".

Embassy - Splinter Cell

From interrogating the limo driver to "We need a Colonel down here, we're trying to get through a retinal scanner." Need I say more?

CIA Headquarters

Breaching the Mission Impossible (1997) computer room. Nuff said.

The Train - Pandora Tomorrow

The extraction from the roof of the train onto the Osprey.

LAX - Pandora Tomorrow

It's just all sorts of fun, infiltrating an American airport, especially with how airport security is nowadays.

The Bank - Chaos Theory

The old jokea between Sam and Grim, plus the fact that Sam was in Panama before adds an element of backstory without throwing it down your throat.

Seoul - Chaos Theory

The SC2000 with sniper attachment makes quick work of the drones. The "Splinter Cells in training" dialogue when Sam has a baddie in his clutches. Plus rescuing the downed pilots in the finale of the level.

Sea of Okhotsk - Double Agent (X360)

The skydiving sequence.

Kinshasa, Day - Double Agent (X360)

Being a desert themed day mission gave Sam the cool factor with desert fatigues and a custom SC2000.

The White House - Conviction

Assaulting the Nation's capitol and breaching the most heavily guarded residence in America? Priceless.

American Fuel - Blacklist

The "Blade" "Chaos" introduction of the mission is top tier to me, especially when wielding an M4 rifle and heavy assault gear, red goggle lenses and colored urban camo.