It's terribly difficult to choose...I'm a huge fan of MKII fatalities mostly, but there are gems in every game truly.
From MK1: Spine Rip of course, Raiden's Head Exploder, Johnny's Super Uppercut, also Heart Rip.
From MKII: Lao's Hat Slice (contender for all time fav), Scorpion's Jugular Cut, Shang Tsung's Soul Steal (it was at its best in MKII), and Reptile's Head Eater (It was so surprising the first time!).
From MK3: Sindel's Scream, Sektor's Compactor, and...that's it really, MK3 fatalities sucked balls.
From MK4: Shinnok's Skeletal Hand Squeeze (So brutal!), Reptile's Acid Bath (ewww...), Quan Chi's Leg Beating (MK4 was kinda lackluster too...).
From MKDA: Scorpion's Head Rip, Hsu Hao's Chest Lazor, Frost's Freeze & Smash (one of the best ice fatalities), Reptile's Acid Bath PLUS Head Eater (Two of my favs combined!), and Cyrax's Chest Grinder, MKDA was a return to form
.
From MKD: Scorpion's Neck Snap, Sub-Zero's Freeze into Sliding Head Pitch (the best ice fatality IMO), Ermac's Telekinetic Rip, Li Mei's Uppercut into Exploding Kick, Shao Kahn's Head Golf (Love that hammer), and Sub-Zero's Leg Freeze & Smash (I love watching the opponent squirm and beg)
From MKA: Nothin'
From MKvDC: Raiden's Grab & Zap, Scorpion's Toasty, Sub-Zero's throwback to MK3 Overhead Freeze & Smash, Deathstroke's Neck Snap, Green Lantern's Ball Squeeze (I don't care what they say, it's fatal I swear), and basically everything the Joker does
.
From MKSM: All of them. Seriously, all of them.
Well..that's my picks by series...if I had to choose my all time fav's tho they would be the Jugular Cut and Lao's Hat Slice from MKII, Both of Sub-Zero's from Deception, Scorpion's Head Rip and Neck Snap from DA and Deception, Toasty!, and The Joker's Fake Out.