Archive Panic: It's a daily comic that ran for 7 years. There are 2658 strips in all. You do the math. (And that doesn't even count the numerous fan comics hosted on the site.)
Ass Pull: Many of the powers and mergings that come about seem to be this, but the Author had it all planned out before, and it is funny.
Ensemble Dark Horse: The Author mentions that Mynd seems to be rather popular among readers.
At one point or more, Dave notes that for some reason he couldn't explain, Shadow Man became exceedingly popular, so of course he had to make use of it.
Proto Man in the future goes by the alias Prometheus, the name of a villain in Mega Man ZX. Proto Man is the epitome of coolness, while Prometheus is more than a little crazy.
In the Mega Man 5 storyline, Stone Man and Wave Man merge into a (quick-drying) Concrete Man. Now fast-forward four years; Capcom makes Mega Man 9, and one of the new Robot Masters is... Concrete Man.
Also, in the Mega Man 4 storyline, Dr Wily is watching a soap opera, and the two main characters are called... Brad and Angelina. This was written while Brad Pitt was still married to Jennifer Aniston.
At the start of "Just Another Day", the storyline that introduces Bob and George proper, Mega Man's irrational fears of "purple floating aliens" are eerily prescient of the alien FM-ians from Mega Man Star Force. These aliens might be anywhere (FM-ians are invisible and inaudible without a Visualizer), float (FM-ians hover), can possess or disguise themselves as people he knows (FM-ians are capable of Demonic Possession), control his thoughts and actions (FM-ians can also invade and control machines), and want to steal his brain. And a few of them are purple.
These supposed 'aliens' also foreshadow the X storyline, where X assimilates the cast. Again, the aliens can possess or disguise themselves as people he knows (X can mimic voices of people he assimilates), float (X floats), and want to steal his brain (which he does).
The X storyline is also similar to Star Force. Previous points aside, X can assimilate robots because his brain is built out of a wireless router. Wireless routers use EM waves to communicate with each other, and the FM-ians can possess computers because they are made out of EM waves.
In the Archie comics, similar to the Sixth Mega Man game parody, Mr. X is a real person and not one of Dr. Wily's disguises.
In the notes for the aptly named "Roll Says the F-Word", The Author self-admitted to restraining from using the word "fuck" for any reason except for once a year, so as to ensure it doesn't become "excessive" and the webcomic devolves into just saying it over and over. While it's mostly dismissed as just a strange writing decision by the Author at the time, over a full decade later, BoJack Horseman would apply a very similar philosophy for the same exact swear word by only using it once a season, though with a different utility and reasoning.
Moral Event Horizon: Zero crosses it in The Cataclysm. In the first episode, he crushes Mega Man's skull off-screen and openly takes pride in telling Dr. Light that he did so. He also gets to kill Roll in Episode 3.
Once Original, Now Common: To be expected from one of the first big sprite comics... Ever. In particular, the author admits to wincing at this strip, even though he knows it's the first use, because writing the author directly into the story as an all-powerful character been done so often in so many sprite comics since.
Tear Jerker: The Cataclysm and how everyone except Proto Man dies.
The Epilogue. Everyone in the Classic period would have died somehow except George, The Author, Ran and Proto Man. George would have been back in his dimension though and he never got to see his friends again and Bob was finally killed at some point. The Author made things worse by giving Ran a more powerful Cossack Buster and because it led to Zero finding Dr. Light, Dr. Light was killed. The Author would then turn into the Shadowy Author and spend the rest of his days blaming himself for the deaths of everyone, as would Proto Man. At least that's how it would have happened had Zero not mentioned that Dr. Wily would be killed by him.
Quick Man is Cut Man and Elec Man's love child on crack.
Values Dissonance: Top Man's Camp Gay portrayal and Mega Man's reaction to it would be extremely problematic in The New '20s. In one comic alone, Mega Man assumes that there were no gay people in 1990 (when Mega Man 3 was released) and that they're "icky". Top Man isn't any better, embodying stereotypes of how the author thought gay men talked and acted at the time. The author, who in-universe calls Mega Man a "fag-hater", simply mentions that he got a good deal of hate mail for it. Changing trends in LGBT acceptance would result in much worse today.
The Woobie: George. He gets trapped in the Mega Man dimension that the Author runs, he gets kidnapped and tied to a ceiling for six months, has Bob for a brother and just goes through a lot of hell throughout the events of the comic.
so of course he had to make use of it.