For TNG, the ones that always remain in memory are The Drumhead, Conspiracy, Yesterday's Enterprise, Best of Both Worlds 1/2, Tapestry, All Good Things, Skin of Evil (because I was in love with Tasha ), and whichever one Barclay turns into a spider in.
EDIT: Oh, and the one about the time loop that begins with Picard yelling "ALL HANDS ABANDON SHIP!" and the Enterprise exploding. Blew my fucking MIND at 11 years old or whatever I was.