No particular order:
Midwinter
It Came From The Desert
Civilization
Pool Of Radiance (or any Goldbox game)
Zak McKraken
(I don't mention Pirates!, because it's the best game ever on any platform, by default, so there's no need
It's tricky, because some of them are ports. If I was to make a list of best Amiga originals, it'd perhaps look a bit different.