Somebody please correct me if I'm wrong, but from my experience it seems that a jump in punch that connects can basically serve as an opener to almost anything... specials, uppercuts, combo fragments, etc.
For instance, Kung Lao's 1, 1, 2, 1 combo... if you wanted to link it with a jump in punch, all you have to do is quickly input 1, 1, 2, 1 after your jump in punch connects. Including your jump in punch, this would count as a 5 hit combo. This works the same with any of the combos listed in the Moves List for any character.
Other things can be linked to a jump in punch too. You could just quickly link an uppercut to a successful jump in punch and it would count as a 2 hit combo. Or you could link a quick special, like Scorpion's spear, right after a successful jump in punch. Stuff like that.