MK2 is by far my most favorite. A great setting and feel to the game. No cute stuff. Fun, creative combos. Each character felt unique. Me and my friends especially liked how certain characters were "stronger" than others. For example, try uppercutting Baraka out of the air. It is damn hard and I have only seen it done with Kung Lao (who has the best uppercut). There are other fun superiority quirks like Jax's air punch and Reptile/Subzero/Scorpion's roundhouse kick which make the game exciting. They removed all of this with MK3 which introduced the pre-made combo system and forced all character's attacks to have the same priority. It just didn't feel right to have EVERY character able to uppercut their opponent out of the air.
The first MK is really great also, but it lacks a little bit of polish compared to MK2. It is a little more clunky feeling and the small number of characters limit variety. Also, Sub-Zero is overpowered.
Ugh, MK Trilogy for N64 is probably the worst console MK game ever. I actually bought it the day it was released and ended up returning it 3 hours later. The music and sound were horrible. It was disappointing.
MK3 for the playstation was one of the reasons why I bought a playstation shortly after release. The only real flaw was that the CD load times rendered Shang Tsung useless.
I have MK4 for the PC and I played a ton of it. They introduced Goro in the home version and for some reason he was exponentially harder than every other opponent, even the final boss. Kind of ruined the fun for me.
I had MK: Deadly Alliance for a while but I just couldn't get into it. Sold it.
I prefer to just play MK 1, 2, and 3 on my PC with MAME. 8)