Long jump when he gets closer, if the energy bar runs out, Double jump then...
If kong Lao: Triangle (x2), Hold Circle
If anyone else: Square (x4), Triangle
I remember Reptile, Baraka and Scorpion to be quite a challenge. The final three bosses were not that difficult, the only difficult thing about them was that you had to face them all with one healthbar.
ordering To hardest:
Shao kahn "No damage"
Reptile "No damage"
Shang tsung "Small Damage and sometimes No damage"
Kitana "Small Damage"
Kano "Small Damage"
The ladies "Small Damage but Annoying and takes Long"
Goro "Small to Some Damage"
Mileena "Small Damage but takes Freaking long and annoying"
Baraka "Some Damage"
Kintaro "Some Damage"
Scorpion "Some Damage+Long and annoying"
Sub-Zero "Some to Medium Damage"
Ermac "Mammoth Damage+Long and annoying"