While Sonic is now sunk too low to meet the expectations of even the average gamer, it was at one time the best of the best, something that gave Nintendo's own Mario a run for his money. Believe it or not, some of the 3d games weren't bad, though most lacked content, had poorly executed gimmicks, and had several flaws that hurt playability. I will list what were my five favorite games, and give a couple honorable mentions.
(Note: I haven't played Sonic Riders 1&2, Sonic Rush (and Adventure), Sonic Advance 1, 2, and 3, Shadow the Hedgehog, Sonic Next Gen, Tails Adventure, Sonic Adventure 2 Battle, and Sonic the Fighters)
5. Sonic Adventure DX
Sonic's famous debut into 3d was initially very well received, but also marked the beginning of the end with its many flaws. Sonic's levels were the main highlight of the game, Tails' and Knuckles' stages were also pretty fun along the side, but Big's felt like a forced, but poorly executed minigame. It also included adventure fields which were later given tons of missions in the DX edition to make it that much more interesting. Unfortunately it isn't quite enough to stand up to the Genesis games. It also featured camera bugs, some relatively linear design for some levels, and the cutscenes didn't always come out right.
4. Sonic 2
Faster than the first and with a whole bunch of new depth, Sonic 2 also introduced Tails as an optional character. With a ton of levels, its hard not to like the game, however because it didn't support any saving, it was all meant to be played in one session, so it started to feel stretched between Casino Nights and Wing Fortress. The final boss also held on to the barely established tradition of fighting without rings which made it painful, especially for a no-save game.
3. Sonic and the Secret Rings
You have to try and keep up with Sonic in this interesting and unique game. With seven worlds each with many paths and alternate layouts to try, it wasn't always completing the level, but doing so efficiently and with style. Time attack is extremely fun to do on most of the challenges and the party games were an interesting add-on. The cut scenes weren't all bad, being somewhat amusing in some places, but a couple boss cutscenes were nearly unbearable, and the secret ring exposition scenes weren't interesting. The on-rails initially doesn't sound great but all these levels still have as much depth, if not more than shown in Sonic Heroes, its a fun game type that I hope will see more sequels; if not from the main series then part of a spin-off series a-la Sonic Riders.
2. Sonic CD
You are given the opportunity to travel through time, the main flaw is that time travel is somewhat cumbersome, but at its best its both an obstacle and a tool. Its an interesting alternate way to achieve the good ending and even if you want to do it the normal way, the special stages are interesting and fun to play. The levels all had a ton of depth and some really interesting gimmicks. The bosses were cool, but in some cases disappointingly easy, Metal Sonic is probably one of the coolest bosses in the 2D series, barring the final bosses of course. Speaking of which, why is the final boss a four-hit wimp who can be defeated within seconds using the temp invincibility?
1. Sonic 3 and Knuckles
This is spot was reserved for this game really. With more depth than ever before, a subtle but decent storyline, cooler bosses, and enough levels to make Sonic 2 look less than amazing while giving you a save feature so you don't have to enjoy them all in one go. Three characters played very, very differently and each could progress through the level with exclusive shortcuts, paths and in some cases bosses. This is also the only Sonic game I've played that has a challenging and enjoyable Super Sonic level while others tend to be easy. The only thing I dislike about this is that I've played it since I first got a gaming console and I have yet to find its match... Additionally it did have its share of frustrating areas, like the underwater Carnival Nights or the Sandopolis sand slides.
Honorable Mention:
Knuckles Chaotix had a very unique play-type which was fun to play around in and actually didn't do to bad throughout the levels. However most of its availability is limited to illegal ROMs or a very dated expansion to the Genesis. Furthermore the levels didn't feel as unique as the other games, each having four acts and all looking pretty much the same. Secret Rings did a good job of keeping the Arabian feel while giving you some diversity, this just had a glaring carnival feel to everything that made them seem identical...
Triple Trouble was my favorite GG title with more depth than any of the others of its kind, and the levels were quite interesting. However, the real reason why it gets honorable mention is because Nack the weasel made his appearance here, as did the epic Sunset Park 3 music.
Also, regarding Heroes, it wasn't a great game, but I enjoyed it. The frequent pits and the cumbersome formation switch made necessary by many areas made it pretty difficult though.