Wonder Boy III, ALttP and SMW are near perfect, I'd say, I can't really come up with anything to complain about at all for those. edit: Okay, I could actually think of two things with WB3: The password system glitches out beyond a certain amount of gold, and the random chance at a potion after dying is a bit bullshit. 
As games have become more complex after that there's been more things that can be at least annoying. Metroid Prime and Paper Mario 2 are probably the two 3D ones that have felt the closest to being perfect to me, if PM2 even qualifies as 3D, hehe. In MP's case it wasn't even technical issues, I just though the space pirate zones and encounters outstayed their welcome.
As games have become more complex after that there's been more things that can be at least annoying. Metroid Prime and Paper Mario 2 are probably the two 3D ones that have felt the closest to being perfect to me, if PM2 even qualifies as 3D, hehe. In MP's case it wasn't even technical issues, I just though the space pirate zones and encounters outstayed their welcome.