Some of the skills from XCOM:Enemy Unknown keep the same names but have modified effects in the Enemy Within expansion.
This question is not asking about new features or abilities from Enemy Within. Rather, it aims to work towards a definitive list of the changes to old skills. I'll start a Community Wiki answer with those that I've spotted so far.
I'm not sure whether any of the old equipment or foundry projects has modified effects, but if so they would be good to include as well.