Ask most people and their favourite Genesis/Mega Drive era Sonic game tends to be Sonic 2. For me however, the third one really epitomises the peak of the Sonic franchise (Though Sonic CD still remains as my favourite). It took some of the best concepts from previous titles and made the mythos of the series more interesting; with Knuckles as a rival, Tails was slightly less annoying as he actually had a function, and the Master Emerald as a pivotal plot point. After this the main plot moved over to Earth rather than Mobius, Robotnik had a makeover which I still don't approve of, and 3D was introduced so I lost interest.
For more Sonic goodness check out my Sonic CD picture -