Many people say Three Leaf Clover but Flatline was the best and the one that sticks out for me. The freedom the mission gave you was insane. You could approach it from many angles (stealth being the one I chose). It was really cool and a different type of mission. Three Leaf Clover was just a generic shootout tbh. Am I the only one who thinks TLC is overrated?
Uncle Vlad was also a really good one. Although nothing special in terms of gameplay, it was the point where the game's story really kicked off.
Flatline was really cool in terms of different approaches although in saying that it's a bummer that no matter if you choice to go stealth or all guns blazing you still end up getting a wanted level either way.
My favourite method is dressing up in the scrubs and pulling Anthony's life support, but it sucks you can't sneak away Agent 47 style like the stealth approach in Final Interview.
It's the only part I dislike, but still a great mission.