I would say its a toss-up between Deception and Armageddon.
MK1: Fantastic game, a true classic
MK2: Like MK1 only darker and grittier
MK3, UMK3, MKT: Okay...I don't really like the run and dial a combo, fun to watch though
MK4: Meh....so-so
MKDA: Pretty good game
MKD: Improved on everything that made Deadly Alliance good, one of my fave MK games ever
MKA: Not a bad game, love the create a fighter concept
MK vs DCU: Actually it was an excellent game and great gameplay, but the DCU made it less Mortal Kombat-y
Never played Shaolin Monks, Mythologies or Special Forces so I wouldn't know...
Overally my favorites would be MK1 & 2 and Deception.