Well, I guess this sections should be called "The bad guys" considering that now, we have a kid as the villan. Oh well, I'll change it... eventually.
Devimon is the first Digimon that they have to defeat. Compared to what they encounter later, he was defeated fairly easily.
He is controlled by Devimon and is forced to battle the kids. He later becomes an ally, and helps them out.
They meet up with Etemon after leaving File Island and going to the continent of server. He thinks that he's a digi-rock star (more like an Elvis impersonator) and want's to rule the digiworld with his dark network. Metal Greymon defeats him and he gets sucked through a hole. He rebuilds himself and gets stronger until he can digivolve to Metal Etemon, then he comes back to the digiworld for revenge. Zudomon and SabreLeomon defeat him.
After beating Etemon for the first time, Myotismon sends Demidevimon to destroy the Digidestined, by making it impossible for their crests to glow. Then he finds out about the eighth child and goes to earth to find and kill him or her. Unfortunately for him, the Digidestined find her first and then he captures her and they fight, it appears that they have won, but he comes back even stronger, and digivolved to Venom Myotismon. It takes Metalgarurumon and Wargreymon to defeat him.
He was cute in his own evil sort of way, but unfortunately, he died...::sniff:: He worked for Myotismon and almost succeeded in stopping their crests from glowing(for a little while, at least). In the end, he was eaten by Venommyotismon. Why the Digidestined would trust any digimon with Devimon is their name is beyond me.
The Dark Masters
These guys that the Digidestined were brought to the digiworld to defeat in the first place. And it's not only the usual, defeat them and save the digiworld, it's 'defeat them and save both worlds'... pretty cool eh?
Metal Seadramon is the Mega form of Seadramon (you'd think it would be Megaseadramon, but noooo, that's only an ultimate... they're purposely trying to confuse us). He is the dark master of the ocean and was beaten by Wargreymon using the weapons on his hands.
Puppetmon is the Dark Master of the forest. He likes to play games and has no friends. That's the one thing that the Digidestined have and he doesn't. He underestimated them, and was defeated by Metalgarurumon.
He's a huge machine-like (duh) digimon that didn't get as many episodes as "the main bad guy" as the rest of them. That's OK, I never really liked him anyway ^_^
The leader of the Dark Masters. Looked like a clown but definitely didn't act like one. He was defeated by Magnaangemon after a long and rather cool battle.
He was the creator of the Dark Masters and a heck of a lot stronger. He destroyed the digidestined's crests, but then they realized that they didn't really need them and kicked his butt anyway.
The Digimon Emperor (AKA Ken Ichijoju)
An evil genius who's goal is to take over the digiworld and control all the Digidestined using control spires to keep the digimon under his command. He recently ran away from home (and his fame!), to rule the digiworld 24/7. He's supposed to be a digidestined... but decided to be the Anti-Digidestined instead.
But before long, he found out that the digiworld was not, in fact, a video game and decided to become a digidestined after a while. Darn, and he was cool as a bad guy too =(