1: Buster Bros. -- Forget about the graphics, the control on the PCE version is very nice (compared to the arcade) and I actually like the Red Book (though many folks may not get excited about it--it is very "happy" and "jovial" instead of having a darker, layered and more nuanced soundscape).
2: Ys III -- you can't tell from the still images, but I always thought that the SNES version did the best job creating a consistent "atmosphere" for the Ys III universe. It seemed, overall, more "refined". Of course, I love the TG-CD version the most (for obvious reasons: Red Book!). The Genesis version is decent, from what I remember.