Teenage Mutant Ninja Turtles: Turtles In Time - Before the Super Nintendo came out, I was a huge fan of the two side-scrolling TMNT games for the original Nintendo. While those were fun games, TMNT: Turtles In Time is an almost perfect transfer of the arcade hit. Gone are the blocky, inferior graphics of previous shooting games —instead the game looks and plays just like the original one in the arcade. It's got a great two-player mode and is one of the best side-scrolling fighting games ever made. I'd argue that it is the definitive side-scrolling beat-em-up game.
Super Castlevania IV - The Castlevania series was popular on the original Nintendo and this debut on the 16-bit Super Nintendo is easily one of the best Super Nintendo games ever. I've spent hours playing this game. It's got a great soundtrack and good graphics—complete with special "Mode 7" scaling effects that show off the power of the Super Nintendo's hardware. There were some changes in the game play, including levels that require you to use main character Simon Belmont's whip to swing across pits.
The Legend of Zelda: A Link to the Past - This was the only game in the Zelda series released for the Super Nintendo, but it is one of the best games in the series. This game marks a return to the overhead perspective of the original Legend of Zelda game and several enhancements. The enhancements include more items, a bigger map, a parallel world, and an even more impressive soundtrack. Technically it's a prequel to the 8-bit games, but the game has a great self-contained story line so you can jump right in without knowing the chronology of the series.
Street Fighter II - No list of the best Super Nintendo games of all time would be complete without including Street Fighter II. Street Fighter II was easily the best of the head-to-head fighting games released for the 16-bit consoles. Street Fighter II triggered the release of a wealth of inferior imitations, but none of them came close to matching the greatness of this game. The game featured great graphics—albeit not quite as good as the arcade version—and addictive fighting games play. In addition to the "special moves" each character possessed, there were a wealth of combinations that could be formed using moves and just the right timing.
