The Chessmaster: His way of telling stories was just a ruse. All of it. The all of the place narration. The unnecessary build up. The fricken cat (sorta), all of them was part of his ruse. A ruse to garner C-waves so he can get back to full power! Hats off to you Mr. Williams.
Glass Cannon: Alex is not overly impressive in terms of durability (though he seems to be getting better, plus, he's usually dealing with top-level opponents). Conversely, his Super Scope is a one-hit kill on anyone.
His sociopathic tenancies are in fact so pronounced that Wily, a publicly-acknowledged villain (turned-unwilling-politician), is already horrified of what he might be capable of via his weapons and equipment.
Hidden Depths: For all his vulgarity and selfishness, Alex is actually very well read.
Trolling Narrator: At least from Ryan's perspective, Alex is constantly this in-universe. Quite a few times during his narration he alluded to secrets that, if revealed, would clarify what exactly was going on, only to make Ryan figure them out himself when questioned about them. He also decided to interrupt his narration of Kain's fight with Schrödinger to move on to something else despite Ryan's loud protestations. And finally, he ignored Ryan asking him to reveal what had happened to Magus and Mario, and later actually moved on to the subject of the Mushroom Kingdom... only to once again talk about something other than Mario's and Magus's exploits.
The Unchosen One: He was told by the shadows from the Desert of Shattered Dreams that he's merely a substitute for the real Game Master (or, as he put it, second best Captain SNES). For some reason when the ultimate warp zone was opened for the first time to let the real Game Master enter Videoland, it got Schrödinger instead. Whether this will be confirmed remains to be seen, but either way Alex is determined to fight the Sovereign of Sorrow.
Walking Pantless Scene: He spent nine years of the comic's run (i.e. more or less a day in-universe) parading around without pants. This finally got remedied by Protoman in episode 694.
Beware the Silly Ones: Mario has... a lot of quirks. But he's viewed with hushed awe by most of Videoland.
Bunny-Ears Lawyer: Despite Magus' complaints and his own actions, Mario knows the nature of Videoland quite thoroughly, is quite dangerous to anyone not enforcing their local reality on him, to the point where even Vegeta refers to him as 'The Great One'. He is rated 9 on the threat scale, the only characters above him are Daos (whose 9.5), and the Sovereign of Sorrow herself. To put this in perspective, the only other threat level 9 character shown so far was an insane end-boss god-being that was tearing Nexus apart block-by-block.
Bag of Spilling: Loses all her power-ups, again. Doesn't stop her from being a badass though.
Combat Pragmatist: She does not care about Eggplant Wizard's plots. She just shoots him in the face with a mega bomb.
Tranquil Fury: Anger gives people the will to resist Sorrow. Samus lost her entire family to Space Pirates and became a bounty hunter as revenge. That said, the only time Samus even seems to lose her cool was as a bid to drive Golbez to rage and fight Eggplant Wizard.
Alex: How she acts and what she feels are two different things. She's disciplined. That's different from being calm.
What the Hell, Hero?: Spoony's reason for revenge on Cecil was because back in Final Fantasy IV, Cecil not only changed his name to Spoony, but also immediately killed him every time he was alive in a random encounter. Though in Cecil's defense, the fault lies with Alex as he was playing the game and controlling Cecil, and he wanted Edward dead because it meant more EXP for the rest of the party.
Back from the Dead: Well, sort of. He does come back after being killed by Amon, but not before turning into Green Mega Man.
Does Not Know His Own Strength: Sort of. While he appears to be well aware of how strong he is, he does not quite know the formula for imparting kinetic energy. When he is told he forgot to square the velocity after hitting Amon, Amon goes from knocked back a few feet, to being launched several thousand fast enough to create a sonic boom, and through a few dunes into a desert that denies sprites their resistances.
Heroic Mime: Like in Crono's case, it's only Alex who can't hear him.
Killer Cat: Even Alex knows his limits, and the greatest of them all is trying to fight Schrödinger, rather than work with him. When Ryan shouted that he could do it, moments after the prison complex lost main power, Alex laughed in his face; for five minutes or so.
Genius Ditz: Alex sees him as this. He comes across as not overly bright, but put him in a situation that plays to his strengths and he's pretty damn good at it. Or as Bass would put it, pretty damn evil at it.
Worf Has The Flu: The reason Vegeta doesn't swoop in and kick Daos' ass is because he's got hypertension and can no longer fight.
Genius Ditz: Dr. Wright has generally been shown acting like a complete moron, but he did reformat Mega Man into his super-strong Captain N iteration and helped build the Gate, which is essentially a Cosmic Keystone which keeps the reality of the desert from completely isolating, if not outright consuming, their universe. In addition, he has more than once realized things that Mega Man didn't — most importantly, the fact that Roll was Sorrow-Touched.
Cosmic Retcon: Episode 771 reveals that one of her powers is the ability to alter the past of those who were Touched. Later strip specifies that she can't alter established events from the past, but she can fill in the blanks.
Eldritch Abomination: Whatever the Sovereign is... she's a powerful super being from god knows where and is intent on destroying the universe. And considering how an aspect of her is able to shrug off the blasts of no less than three godlike entities without noticing as well as warp reality to her benefit, she seems capable of doing so.
Flashbacks to when she was at full power make this even more clear. At that time, she was able to annihilate entire game worlds with little effort, if any.
A Form You Are Comfortable With: Mortals cannot see the Sovereign of Sorrow in her true form, and can only interpret it. When Magus encounters the Sovereign of Sorrow, she appears to him as Queen Zeal. Gods like the Sinistrals are able to pierce the illusion and see a noblewoman wearing a mask. Her silhouette is eerily similar to Schala's.
Bunny-Ears Lawyer/Obfuscating Stupidity: He's either putting on an act to get people to underestimate him, or he using his annoying, hyperactive personality to put people off. But he's pretty damn dangerous given his access to the environment systems.
Body Snatcher: He cast a spell on the survivors of the Argo that made it possible for him to do this. Whenever he gets killed, he just takes over one of the survivors' bodies and transforms it into his own - while his victim dies in his place. This saves his life in a fight against Samus Aran.
Evil Gloating: Tries this twice on Samus Aran. Gets shot in the face and frozen solid for trying.
Gone Horribly Wrong: His attempt to Mind Probe Samus not only has her breaking him, but she also plants a telepathic suggestion that eventually makes him break her out.
His Mind Probe on Golbez also doesn't work out so hot.
Sharing a Body: As a result of snatching a body of yet-unknown Touchedsomeone, who not only survived it but also was able to reclaim the control of the body.
''Soon my dear Rose, you will be mine!"
Badass: Spoony at least is confident that Kain would have no problems defeating both Crono and Cecil. Plus, so far all his fights with opponents other than Schrödinger (i.e. Cecil's guards, Bikke, Gato, Alex, the population of the Mithril town and two of Eblan's most elite ninja) ended with Kain curbstomping them.
Berserk Button: As the population of the Mithril town learned the hard way, he really hates being mocked.
Unwitting Pawn: As a part of Spoony's plan to summon the Sovereign of Sorrow Kain was ordered to kill Bob. He ended up being tricked by Bob into thinking that Bikke was Bob in disguise, letting him go (and eventually help Alex escape from prison) and killing Bikke. Spoony wasn't too happy about this.
Small Name, Big Ego: He seems to genuinely believe that he's unbeatable and that he'll succeed in all his plans. Those 463 times Mario's beaten him up? Beginner's Luck! Obviously he will win the next time!
Out-Gambitted: The Sinistrals wanted to get the Shard of Tears because the Sovereign of Sorrow told them it would give them power over her, which in turn would allow them to free Erim from her influence as well as make them practically invincible. They went to the Nexus because the Sovereign told them that's were the Shard was. She also told them that the Gamemaster is her champion, so when they met Alex in Nexus they wanted to kill him or at least make him serve them. It looked like the Sinistrals were on their way to become the Big Bads of the story... until Alex pointed out that going to the Nexus and fighting him was exactly what the Sovereign wanted them to do, as it meant that her enemies, instead of trying to fight her, would fight against each other. Which is what ultimately happened - Alex ended up killing two of the Sinistrals, but not before learning that he couldn't oppose the Sovereign without paying a price.
Pride: One of their defining traits. As Alex pointed out, upon meeting someone who's more powerful than they are or at least refuses to bend to their will, the Sinistrals just refuse to let it go; their arrogance blinds them and they can only think about killing or subjugating their opponent. This eventually leads to Daos's and Gades's undoing and to Amon being trapped on the Desert of Shattered Dreams.
Your Mom: Mega Man manages to enrage Amon by saying this. Why a physical incarnation would be so agitated over this is a mystery, seeing as how Amon doesn't actually have parents.
A.I. Is a Crapshoot: Although Gato is well behaved at first, Kain did serious damage to his programming with a well-placed spear to his processors. Before being Touched, he was an HK-47 wannabe with a micro-singularity. Now...
Humans Are Bastards: Considering Gato was created to be beaten up, and he's the easiest way to get Silver Points, and you have to get 40 Silver Points to resurrect Crono, you can start to understand him.
Ax-Crazy: This catches anybody doing ANYTHING he thinks is drug related, he solution, KILL THEM.
Insane Troll Logic: During their confrontation, after Mario dodges his bullets and teases him for it, Max Force claims he did not miss Mario because he was actually shooting a drug tree, invisible drug beetles and drug-filled air molecules.
Mind Probe: Subjected to one by Magus, whom was attempting to find out just what happened to him. Ended up as a...
Mind Rape: When Magus tried to dig a little too forcibly.
Sliding Scale of Idealism Versus Cynicism: Pre-Great Change/Touch, he was incredibily idealistic. Pre-Touched Max was more than willing to fight an impossible battle not expecting to win, but because its moraly right. Post-Great Change/Touch on the other hand...
Obfuscating Stupidity: The entire Drab Lord persona is this. By presenting himself as a buffoon, he not only causes potential threats like Rydia to underestimate him, but it also helps him keep his sanity despite being Touched, through giving him something to laugh at.
Villain Forgot to Level Grind: Due to Alex playing FFIV and ordering Cecil to kill Spoony every time he was alive in a random encounter, the only EXP Spoony obtained was in his only mandatory story battle, otherwise he remains at the same level that he joined the party in the game. As a result, he can't even touch Cecil, since Alex level grinded him to Lv99.
Ryan (Alex's captor)
Divided We Fall: He can't exactly be called truly evil. Both he and Alex want to protect the Videoland, but that doesn't stop them from fighting over which one of them should be the Game Master.
Gosh Dang It to Heck!: He hates Alex's tendency to swear and tries to either completely avoid swearing himself (he even refuses to say 'bastard') or at worst use very mild (like 'heck') or made-up cuss words.
Ambiguously Evil: He seems to have some goals he wants to accomplish, but we have no idea what they are or whose side he is really on. The fact that he likes to keep Alex in the dark, pretended he couldn't talk after being turned into chocobo, avoided any contact with Alex after being turned into Juan Valdez and apparently is in contact with Wily surely doesn't make him look particularly trustworthy.
The Chessmaster: Has shades of this: He managed to track Alex's movements for a while (but Schroëdinger blew up his plan) as soon as he reached Videoland, he played mind games with several protagonists (including Mega Man), he's (presumably) responsible for the discovery of Ω energy and overall he seems to know way more than he lets on, having several plans in motion. He designed multiples dangerous weapons such as the S.C.O.P.E, ammunitions for Alex's Super Scope, and could very well OHKO Alex if he decided to, thanks to the aforementioned S.C.O.P.E. Definitly one of the most dangerous character down here, though clearly outclassed by the Sovereign.
Enemy Mine: He gladly joins forces with Dr. Light, since there's no point in taking over Videoland if the Sovereign of Sorrow destroys everything. However, it's pretty obvious that he's simultaneously plottingsomething (most likely) evil.
Kicked Upstairs / Be Careful What You Wish For: Sure, he is vice-president of Videoland... but the president is Popular Is DumbMike Haggar, who even abolished every tax in Videoland and transformed the presidential palace in a motel to earn the governmental budget. As of Wily's most recent estimates, they're only $99 billion dollars in the red. Wily has to spend all his time trying to minimize the damage caused by Haggar's decisions.
Punch Clock Villain: He was working for Mother Brain not because he wanted to take over Videoland or anything, but because it paid the bills. Despite being beaten up and humiliated time after time again by Captain N, King Hippo never held anything against him (he actually respected and admired him), and is rather grateful that Captain N didn't either.