- Wager Master (immortal master of games)
- Gloomweaver (extra-dimensional spirit of magic)
- Tachyon (genius scientist and inventor)
- Baron Blade (mad genius, probably right at Tachyon's level or above)
- Grand Warlord Voss (alien scientist)
- Parse (data analyst with upgraded mental abilities)
- Omnitron-X (advanced AI)
- Omnitron (same as Omnitron-X, really)
- Wraith (brilliant CEO and inventor)
- Chairman (brilliant CEO and inventor)
- Unity (natural inventor)
- Writhe (inventor)
- Deadline (endling scientist and mystic)
- Zhu Long (ancient mystic, possibly non-human)
- Biomancer (ancient wizard)
- Nightmist (detective and magic prodigy)
- Anubis (ancient divine judge and master of magic)
- Bunker (tactical prodigy)
- Tempest (ambassador and scientist)
- Ra (a wonder in his field)
- Operative (intelligent enough to get the Chairman's attention)
- Friction (one of Tachyon's interns, but whose inventions don't actually work)
- Haka (undying mystic, teacher; very well read) [edit: adjusted as per Foote's comment]
- Ermine (greatest thief in the world)
- Naturalist (successful businessman)
- Atum (tomb raider, leader of Ennead)
- Shu (Ennead mystic)
- Osiris (Ennead mystic)
- Isis (Ennead mystic)
- Set (Ennead mystic)
- Dr. Medico (med school)
- Captain Cosmic (law school)
- Visionary (psychic training, high academic test scores)
- Dreamer (same intelligence as Visionary, really)
- Ambuscade (gadget based villain, but not an inventor)
- Scholar (lots of folk wisdom and mystic knowledge)
- Chokepoint (talks to machine, seems to have some sort of mind-expanding experience)
- Blood Countess Bathory (old and probably well-read)
- Sky-Scraper (freedom fighter and saboteur)
- Legacy (natural leader and tactician)
- Iron Legacy (same as Legacy, really)
- Nuit (guardian spirit of the Ennead)
- La Capitan (smart enough to navigate a time ship)
- Citizen Dawn (natural leader; careful planning)
- Miss Information (administrative assistant with in depth knowledge of the heroes)
- Absolute Zero (college graduate turned janitor)
- Benchmark (no idea yet, but if his head is partly computer, he probably has brain enhancements)
- Young Legacy (expert tutelage)
- Kaargra Warfang (no real idea how smart she is, but she does run a colloseum, so probably not dumb)
- Nephthys (healer and destoyer)
- K.N.Y.F.E. (highly trained agent)
- Mr. Fixer (skilled mechanic)
- Chrono-Ranger (old west sherrif)
- Greazer Clutch ("above average" alien bounty hunter)
- Expatriette (cunning tactition)
- Sergeant Steel (dangerous F.I.L.T.E.R. agent)
- Proletariat (exemplary soldier)
- Fright Train (skilled soldier)
- Tefnut (warrior of the Ennead)
- Kismet (thief; likes playing mind games)
- Infinitor (was a police officer before going mad from cosmic energy)
- Apostate (Fanatic's dark mirrior; seems slightly more devious)
- Fanatic (stubborn and pious)
- Citizen Hammer (seems cocky and brash, but is based on a wizard archetype)
- Citizen Anvil (careful and elusive, but based on a paladin archetype)
- Argent Adept (musician and bartender)
- Matriarch (goth poet)
- Idealist (middle schooler with psychic powers and a wild imagination)
- Mainstay ("meat-head football player," but smart enough to finish college)
- Guise (Guise)
- Setback (lovable loser)
- Geb (known for raw destructive power)
- Bugbear (hired muscle turned primitive monster)
- Spite (drug addled serial killer)
- Progeny (alien force of nature that never speaks)
- Akash'Bhuta (raw force of nature, none of her cards quote her actually saying anything)
- Plague Rat (somewhat above animal intelligence)
(I expect to be told that I'm way off on some of these, and how) ;-)