Aborted Arc: Not directly in the comic per se, but the 'Cataclysm' side-story is a good example. Referenced in-comic by X, Zero, Protoman, and Bob; meant to explain the intentional gap between the Mega Man (Classic) and Mega Man X series, with the plot being that Dr. Wily's building and premature activation of Zero, causing him to systematically kill and destroy every member of the Mega Man continuity. Originally planned to be animated multi-part flash movies, according to Dave himself, they became "A lesson in frustration for everyone involved." Eight episodes were planned, but less than half of them ever saw the light of day, due to the project stalling out and Anez's life progressing towards adulthood. Anez himself has stated that he'd like to finish them one day, but "I don't really know if that day will ever come."
Almost every anniversary party chapter can be seen as a crossover between the main Bob and George comic and the many comics that are hosted on the site.
Crouching Moron, Hidden Badass: Mega Man; ordinarily an idiot, but he often develops quite clever strategies whenever he heads into battle. His programming states that stupidity is a secondary objective, and he ignores it while performing his primary task - fighting stuff.
Cut Himself Shaving: After the Shadowy Author revives dead characters in the Rockman Universe. Bob tells Rock and Dr. Light that they fell down. Rock then questions if Roll fell up, as she's tied to the ceiling. Bob responses that he put her up there to prevent her from falling down.
Does This Remind You of Anything?: In the comments for a battle between Snake Man and Ring Man in the 6th games Robot Tournament, Anez admitted that he ran out of amusing filler robots with some relation and just threw in the two least quirkiest robots for that day's comic. The next day he commented on how many e-mails he got explaining "the obvious relationship between snakes and rings."
Doomed by Canon: Even though most of the cast get killed during major storylines (such as in "The Attack of Mynd") and get better once they're over, it seems as if the Cataclysm would be their Final Deaths. Then it turns out that they merely faked their deaths, making this trope a subversion.
Early Installment Weirdness: Early on there was a Running Gag about the characters complaining about having to take part in the comic. This was slowly dropped as the comic went on since Dave Anez felt having the joke would just get more and more stale.
Evil Counterpart: As in the games, Bass to Mega Man. Though in this case, Wily went a little too far in having Bass one-up Mega Man in everything. Yes, he's stronger and faster...but he's also stupider.
Expendable Alternate Universe: The Rockman Universe and the alternates in the final battle, who are sent out in droves. Averted in the case of George himself, who does care what happens to the Mega Man universe despite not being from it.
Forgot I Could Fly: Note: do not point out to a character who has spent six months suspended by his arms in Dr. Wily's fortress that he has superpowers and could have escaped. Mega Man also often forgets he can teleport, although subverted in one occasion he is badly injured and forced to crawl to his base due to the fact it was broken.
At one point, Mega Man actually frightened his intelligent alternate self with his sudden battle brilliance.
Get a Hold of Yourself, Man!: George and Proto Man stumble across a VHS tape of the First Annual Robot Tournament (the events leading to Mega Man 6). Turns out, it's just a documentary. But George really wants to find out what happened:
George: There's only one way to find out what really happened! We have to go back in time! (Proto Man slaps George across the face) (Beat) George: ...did you just bitch-slap me? Proto Man: Yes. You needed it. George: Yes I did. Thanks.
Identical Twin ID Tags: The alternate future and alternate far-future versions of Bass and Mega Man wear nametags, thanks to the Author's intervention. Then the alternate far-far-future versions of Bass and Mega Man arrive with similar name tags...and then take them off, revealing themselves to be the present-day alternate Bass and Mega Man.
Commentary: Wow, who would've thought that all of the Robot Masters would just be standing around in a big field together in the middle of nowhere where Mega Man could just conveniently run into them? I mean, seriously, aren't they supposed to be out trying to Take Over the World or something?
Indy Ploy: Pretty much the entire comic, according to the author. In the comments section he admits that he was basically winging the entire thing, and whenever he created a plot hole, he was willing to go to absurd lengths to fix them, introducing time travel, clones, etc... rather than just let the hole remain.
In Medias Res: The Attack of Non-Alternate Mynd starts off this way. While previous events had lead up to this, the actual series of comics starts off with George, Protoman and Mike standing on a pile of corpses, fighting, with no explanation as to how they got there. Mynd asks George to explain How We Got Here.
Nice Job Breaking It, Hero: Dr. Light's entire pathos with X is this. He meddles with X's programming to the point where he makes him an antisocial wuss who is pacifistic (resulting in a botched plan by Proto Man and Roll to steal his blaster) and hates ice-cream (making it impossible to make friends with people, especially George, Chadling and Mega Man). After a off-handed remark by George that he can't force people to be his friend, X goes nuts and does exactly that... with a little help from the wireless router Dr. Light used to build X's brain.
Later, it's given a Double Subversion. Bob and George can't die because they're in the title of the comic, so when the plot calls for George to actually die, the title of the comic changes to allow it to happen. He gets better, though, and the title returns to "Bob and George."
Real Life Writes the Plot: During July 2003, the Author had not only lost his internet connection, but the site also suffered a server crash. In the following month, he had to play catch up, resulting in many of the punchlines being mediocre, to the point where the author actually apologises in-comic.
Recap Episode: There's quite a few of them, most notably "Story Time".
Right Behind Me: Happens to Wily all the time. Subverted at one point, where no one was behind Wily, and he complained it just wasn't the same.
Inverted during the final storyline, where Bob (who at this point believed he killed Wily) boasts that Metool-D2's shield won't stop his Robot Master army, at which point Wily appears behind Bob to have a say on the matter, revealing that Bob only killed a robot decoy.
Super-Powered Robot Meter Maids: Parodied during the adaptation for the first game, where all of Dr. Light's robots seemed suited for combat, but are all designed to do mundane household chores (Proto Man's a butler, Cut Man's a gardener, Ice Man lives in a fridge, Guts Man's a garbage man, Fire Man manages the fireplace, Elec Man powers the TV, and Bomb Man... is just a love machine).
Take That: According to Anez, some fans complained about the characters' dialogue being to stilted and too Superfriends-sounding. He then wrote a comic in which the characters spouted William Shakespeareian dialect (appropriately titled "Mega Hamlet", as Bob had wandered into a Shakespeare-influenced universe), leaving Bob to note, "Well, at least they don't sound like something out of Superfriends..."
Too Dumb to Live: Inverted. Mega Man has the "extraordinary ability to not recognize life-threatening injuries" — he's too stupid to die.
Played straight with many of the robot masters, though; Bubble Man in the game tries to make you jump to the top of the screen with the Deadly Spikes. In the strip, all Rock has to do is do bet him that he can't reach the spikes.
Trademark Favorite Food: Chadling, George, and Mega Man will find a way to get ice cream whether it involves betraying their employer, ruining continuity, or suffering the side effects of massive dairy consumption while lactose intolerant.
Chadling initially loved bananas, but that was quickly traded for ice cream.
Bob also mentions, almost in passing, during one of the hand drawn strips that he love BBQ. When he is the Big Bad of the last plot events are just kicking off before the 4th. He tells all his robots to stand down. The text during the celebration shows that he only did so because he seems to enjoy a good BBQ almost as much as George loves ice cream, and will take any excuse to start up the grill within sense.
Trope Codifier: Did not create the sprite comic, but did set a lot of standards for them.
Weirdness Magnet: If the Author appears, weird things 'will' happen to whatever universe or timeline he's in. At one point a character in the future complains that because the Author hadn't showed up for years in his timeline, things have gotten boring 'and' he hasn't had a good reason to smirk for ages.