Ecco the Dolphin for Sega Genesis…a dolphin fighting aliens and saving the earth. It had like 30-something levels (one level’s title, ‘Welcome to the Machine’…the Pink Floyd reference just makes it that much cooler) the puzzles were fun, and the dolphins are cute, too. ^^
Ecco was great, even though I have to this day not completed every level (I have beaten the game using passwords). Ecco 2 is even better IMO. There are many interesting things you get to do in 2 that weren’t availible in the first one.
Legend of Mana, Kid Icarus, and the Lufia series aren’t lesser known. The latter two of those were once great, but faded.
Commander Keen, especially 1 and 4.