In Desert Island Disks style my favorite episode I would watch would be Summer of 4 ft 2.
Fantastic episode which shows Lisa making friends, being confident, being happy and in different clothes too (i like to see here in different styles). Also it contains Bart actually realizing he went too far and doing something nice for her, showing that he really does care deep down.
If that episode wasn't available it would be Moanin' Lisa or Lisa's Wedding.
Yes, that was a real beautiful episode with a surprising end - I didn't thought, even if I hoped, they would do such a thing for her.