So, you wanna know how the comic is made, do you? Well, I hope you've got a snack, this may get kinda lengthy...
I always start with a template, just the black border around the whole thing. Depending which story arc we're on, I might have a different template saved. For the Maniac Mansion arc, I had a template that had the black borders and all the text for the different commands already there, all I had to add in was the various rooms. For the Lolo arc, I had a template that has slightly more black space around each panel. This is simply because normally, I grab a 196x196 section of a game and double its size for each panel. With Lolo, however, I couldn't get any 196x196 portion that didn't have weird bits sticking out on both ends, so I just grabbed a 192x192 box to get the panels. With the panel size I decided to go with, I can virtually never grab all of a game's screen. (Although, in some games, like Castlevania, that have status bars that take up a third of the screen, I have the opposite problem and have to fill things in with tons of black space.) For a lot of games where the characters stay in one area for long periods of time, I'd just create the background and save it, so I wouldn't have to recreate it day after day.
Once the background's set, I add in my own characters. In Paint, it's as simple as copy/paste. A little trick that not many people know that Paint can do is making certain colors transparent. There's a button you can switch (or, in Windows 7 Paint, a Transparent Selection setting that can be checkmarked) that sets the right click color to be transparent, which lets you paste in just the character, rather than the character and the color around him. Placing the characters then just becomes a matter of zooming in close enough to set them on the right pixel (usually, sometimes I don't care enough to do this). After the main characters and minor characters go in, I fiddle with the ones inherent to the game, like the Goombas in Mario or the enemies in Lolo. If there's any special effects to do, like characters being blurred or anything like that, they're done at this point, in the GIMP.
Once all the effects are done, the text goes in. I pull the screen over to the right and write all the text outside the comic, it's very, very bad form to write the text right on the comic itself. Usually, I'll have at least some idea of what I want the characters to say. On very rare occasions, I'll actually have something storyboarded and know almost exactly what everyone says. Nine times out of ten, though, I'm just making it up a few hours before the update. After it's written, the boxes go around the text and it's placed in the comic, much the same way the characters are. This often leads to me having to re-write the text and space it out differently to fit it into a certain place in the panel. In comic 429, for example, Draco's line "I can hardly get around this place" was originally written to just be on two lines instead of three, but it wouldn't fit anywhere like that. I also have a file called Temp that I'll use if I'm half done with a comic and need to shut down Paint for whatever reason, and also Temp 2 that I'll use if I have a comic with a two frame animation.
After all that nonsense is done, the comic is essentially finished. Certain special effects that can't be copied from the GIMP into Paint are done at this point, but there's not very many of those. Oh, and if something in the comic is animated, any of these steps can be tossed out of order. As a random example, in the comic where Ace placed Kirby in a Barrier, Kirby was the last thing I put into that comic, so I could just hit ctrl+z and stick the second Kirby (with the different Barrier sprite) in the same place, and save it as a separate file. I use Blumental's Easy GIF Animator for all of my animated comics, it's worked amazingly well for anything from a two frame comic to something huge like Kaid's introductory comic.
After the comic is complete comes the only part I don't much like doing each night... coming up with a title and a comment for it. If they seem like they have absolutely no thought put into them, or just seem random and arbitrary and reveal nothing insightful about the comic itself... Now you know why. Usually, I come up with them in the few minutes it takes for the server to load while I'm updating.
Well, that's pretty much all the secrets of how the comic is made, hope that answers any questions you had (and probably several that you didn't have).
All material not © Acclaim, Bandai, Capco, Data East, GameTek, Hal, Hudson, Irem, Jaleco, Kemco, Konami, Lucasfilm Games, Milton Bradley, Namco, Nexoft, Nintendo, Rare Ltd., SNK, SunSoft, Taito, Technos, Tecmo, Tradewest, or any other video game company that I may have forgotten, © Alex Puotinen, 2003-2013.