Intended to be the second half of Sonic 3, but you could make the case that this released as the fourth mainline game due to its standalone capability.
Sonic the Hedgehog: Triple Trouble
Not as much as the fan remake, but Knuckles does reappear…
Sonic Crackers
Knuckles' Chaotix
Sonic the Fighters
Sonic Blast
Sonic 3D Blast
Sonic X-treme
Sonic R
Sonic Robo Blast
Sonic Jam
Sonic Adventure
Sonic the Hedgehog Pocket Adventure
Sonic Advance
Sonic the Hedgehog 4
No.
Sonic Generations
(the 2D half of the game)
Sonic.EXE
joke entry obviously, but i mean… it uses sonic 3 gameplay sprites, it introduces a new playable character and brings back all the existing ones… technically!