Even though I'm more of a Capcom / Street Fighter fan, I enjoyed some MK back in the day. I played MK1 through MK3 quite a bit inbetween bouts of SF2 at the local arcades, though got sort of bored with the series by the time UMK3 came out, and never really bothered at all with MK4 or anything after that.
Anyway, I played pretty much every character, but here's what I'd have to say were my overall favorites / most used characters...
MK1 - Johnny Cage and Kano
MK2 - Johnny Cage and Kung Lao
MK3 - Sonya Blade and Kurtis Stryker
As a bonus, since I played it pretty extensively and competitively, I'll list what I consider the character tier lists for the arcade versions of the first three MK games. Feel free to ask me about my reasoning behind any of them if you're wondering.
MK1
Top Tier - Johnny Cage, Kano, Raiden
Middle Tier - Scorpion, Sub Zero, Liu Kang
Bottom Tier - Sonya Blade
MK2
Top Tier - Kitana, Scorpion
Upper Middle Tier - Kung Lao, Liu Kang, Johnny Cage, Jax, Shang Tsung
Lower Middle Tier - Sub Zero, Baraka, Raiden
Bottom Tier - Reptile, Mileena
MK3
Top Tier - Kabal, Smoke, Sonya Blade
Upper Middle Tier - Shang Tsung, Cyrax, Jax, Kano, Kung Lao
Lower Middle Tier - Sindel, Sektor, Stryker, Nightwolf, Liu Kang, Sub Zero
Bottom Tier - Sheeva
UMK3
I don't remember it well enough to post an entire tier list, but I remember Scorpion and Kitana were top tier again, the other ninjas were pretty strong, while Kabal and some of the other stronger characters from MK3 got nerfed, except for Sonya who was still top tier and possibly even a little better than in MK3.