I base my opinion mostly on how easy/satisfying they are to throw.
#1: HL2: Easy to throw, super satisfying. Bonus points but not a decider, Grav gun+grenade adds more.
#2: CS: Also usually easy to throw but not quite as easy but also satisfying. Mostly flash and smoke though HE kinda sucks now.
#3: Halo: Bouncy, they go where you want. Plasma grenade is incredibly satisfying.
runner up: Red Orchestra/Rising Storm: Throwing them sucks but damn getting 6 kills because everyone is huddled is incredible.