Before plotting, you need to decide on act structure. Before you can do this, decide on how you want it to end: On a good note, or a bad one.
If you want the standard feel-good ending, then the last act needs to be a rising action; basically, it needs to have been bad, had something good happen, and rise from there. If you want the bad guys to win, then it needs to have been going good, then something bad happen, and it goes down from there.
Those points are called "climaxes". It's when you have risen or fallen as far as you can, and have started going in the opposite direction. Assuming a standard three-act play, the action will rise, hit a climactic point, and then start falling. It will hit a second climax, and the action starts rising again.
It'll sorta look like this (if you plotted it in terms of positive actions (things go good for the hero) and negative actions (things go bad for the hero)):--+------- -+-+------ +---+---+ -----+-+- ------+---
A bad (ie, not non-good, but more "bad guys win" ending needs the opposite: A falling action, then rising action, and back to the falling action:-------+-- ------+-+- +---+---+ -+-+----- --+-------
Note that I'm assuming a standard three-act play; most movies are based on them. The beginning is short (about 10-15 scenes, or 20-30 minutes), the middle is twice as long (about 2-30 scenes, or 40-60 minutes), and the end is as long as the beginning (about 10-15 scenes, or 20-30 minutes).
For a comic, the same basically applies; think about it: First act is when the heroes find out about the problem, and by the end of the act are either forced to deal with it, or have decided to deal with it. However, then various plot complications come to play (why they can't succeed, or why they shouldn't, better known as "The Quest"); this is the second act. When they can finally start being able to deal with the issue, that's the third act.
This is not to say you can't add on new acts; just keep in mind that they should keep up the pattern (otherwise it's just a continuation of the current act!).
This isn't to say you need to keep up the pace; it's good to vary the pace. I'm not talking battle-chase-cliffhanger; that's keeping the pace on high. I'm talking, battle-catch breath-chase-regroup-cliff-hanger. Ever been on a roller-coaster that never lets you catch your breath? Bored at the end? The same applies to stories; you need the audience to catch their breath or your breakneck pace story ends up being boring.
Throw in the subplots, the running gag, and don't be afraid of exposition! People don't like exposition because they see it as "the boring parts"; when it's done badly (just talking, or a Q&A session), then it does nothing, and it is boring. But, with as a flashback, or with the proper graphical back-up, or even when it's virtually asked for, it can be great.
Oh, yeah: Plot vs. Character. This is sort of a weird one; there's a debate going because there are two groups out there that believe one or the other is better. The "Plot is better" group think that the plot should go not change no matter what after you have written it. The "Character Rules" group believes that plot should change as you find out more about the characters.
Personally, I'm a fan of not forcing a character to do anything that feels unnatural unless you can justify it. Plot First types generally don't allow for characterization beyond needed for the plot; should something come up, the plot comes first and won't be changd. Character Rules groupies have no problem changing the plot to facilitate characters, but that gets annoying after a bit to readers. Thus, I go with the compromise to not change what I'm doing unless it feels right for both plot and character, with an edge for characters.