Polnareff is a great shout for this, a lot of people call that part Polnareff's Bizarre Adventure because of how much focus he is given. He serves as both the emotional center for that part and the main source of the wacky characterization that JoJo's is known for. I like his penultimate battle against Vanilla Ice more than the final fight with DIO myself. JoJo's a pretty great series for this stuff too, though if I had to pick my favourite it be Bruno Buccellati from Golden Wind. You could definitely argue that Bruno's the actual main character there instead of Giorno.
Those two play a role for the vast majority of their series so you could probably argue that they're main characters even if they're not *the* main character. Characters I really like that don't have any claim to main character status would be Gaara from Naruto, Hayato from OreGairu, Kiromaru from Shinsekai Yori, Wenge from Ping Pong the Animation, Tokoyami from My Hero Academia, and a lot from HxH but I'll go with Komugi & Ging Freecs. Tried to avoid villains for this.
My two favourite side characters though are probably Roy Mustang from Fullmetal Alchemist and Wolfgang Grimmer from Monster. Two of my all-time favourite characters in any media.
