Super Metroid
Majora's Mask
And...this might rub some people the wrong way but...Paper Mario; just has an awesome feel to it.
Actually, while we're on the subject of stuff that might get a raised eyebrow...Super Mario Land 2: Six Golden Coins.
And...Touhou has a bunch. Utshuo Reuji from 11, of course. Remillia from 6. Yuyuko from 7. Those are among the top 10 bosses in a series that is all about bosses.
Final Fantasy X. Stands out for just the impact of the scene, but also for the fight that can be brutal if underleveled.
Koudelka is...damn memorable. I'm not sure if I'd call it good; I have mixed feelings, but it's sure as hell attention grabbing and memorable.
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Cats land on their feet. Toast lands peanut butter side down. A cat with toast strapped to its back will hover above the ground in a state of quantum indecision