In order of appearance...
Esswood A (エスウッド・A Essuuddo): Called Chief Esswood by Jester and Director by a nameless scientist, he appears to be in charge of the Majesty mines in the Chipeya Mountains. He and Jester have a conversation at the start of the game, where they throw around terms that won't be explained till the end of the game.
Jester R (ジェスター・R Jesuta): Mentor to Ark and Ivy and one of the Gate Guardians' Six Stars. He is widely looked up to, and everyone seems relieved that he's with their group. However, early on, he sacrifices his life in an attempt to kill Pike Nighttrap, but nothing comes of it because he didn't have the Plug to resonate with his purple majesty. His age is 25 in the US release and 24 in the Japanese release.
Pike Nighttrap (パイク・T・N Paiku): Member of the Crimson Nine, he's had at least one encounter with Jester in the past. It is Pike who is responsible for both the group's being trapped in the first place as well as separating them after he kills Jester. All of the other builders seen in-game are his subordinates. In the Japanese version of the game, his name is written as "Pike The Nighttrap" (パイク・ザ・ナイトトラップ Paiku Za Naitotorappu), making it a title rather than a last name.
Captures... The entire group aboard the Blue Creek.
Genox (ゼノックス Zenokkusu): He may act like a goofball at times, and have some of the strangest mannerisms, but he's still a builder CIMA. Genox is obsessed with Dragons, and all but one of the dungeons he rules over have some type of Dragon as a boss (the one that doesn't has a dinosaur so it's close enough). Though he has a few moments of strong intelligence throughout the game, most of the fans remember him for his goofy behavior. His in-battle form is a Dragon that can either ride around in a cloud or turn into a shuriken, and is powered by giant Diamond Majesties.
Captures... Halley, Emmy, Philis, Jean, Telmia.
Elvira (エルヴィラ Eruvira): AKA "Token Female Baddie." Elvira seems to enjoy arguing with Genox and trying to see which one of them is better. Though sometimes, just like with Ark and Ivy, it's hard to tell whether the two of them like or hate each other. Her in-battle form is a giant spider with the head being replaced by the torso, arms and head of a woman.
Captures... Vanrose, Eberle, Diana, Claude.
The Villagers of The Village of Rooda (ルーダの村 Ruuda no Mura, lit. Ruuda Village): While I usually don't list nameless scrubs in this type of an article, the village as a whole deserves special mention for A) being the only village you visit all game and C) how much of a parody it is. Conjured up by Genox to go along with Dragon's Dungeon, it features people who say the same thing over and over again no matter how much Ark and Ivy question them for information, leading to a hilarious scene of Ark yelling at a constantly repeating villager. Just like a stereotypical RPG, the Elder gives you a long-winded riddle that boils down to "Go save the sacrifice from the Dragon" with the sacrifice in question being Emmy. Needless to say, once they have the information they need, Ark and the others are running quickly towards the cave in back where the Dragon dwells.
Falcken (ファルケン Faruken): A big bruiser of a CIMA who delights in the pain he causes. It was Falcken who killed Doug's daughter twenty years ago, and Doug's anger at the fiend is even worse than his at the Gate Guardians. Not that Falcken cares about that. His in-battle form is a trio of Doom Trains.
Captures... Doug, Yurald, Ileyda
Sawma (ソーマ Sooma): The last of Pike's warriors, Sawma seems just as eager for a fight as Falcken but a lot less mean about it. Being the only CIMA without a connection to either his fellow builders or one of the group members, little is known about him. His in-battle form is that of a giant samurai.
Captures... Shelley, Rick, Genox disguised as Jean.