Heh. Just realized that I forgot to mention themes.
Oops. So...backing up a step...
The theme is the arguably the most important part of the comic. You'll find that a theme does one thing really, really well for you, and that one thing is extremely important: It ups the importance of your comic. By making it a lesson, you make it important for other people to listen to you, because YOU HAVE SOMETHING TO SAY!
Think about that for a moment. By deciding the core of your comic, by deciding on what you want to say, you add something to you comic.
Better yet, it allows you to remain focused, and centers your imagination. As you are trying to figure out what needs to be done, you have something that helps you to concentrate the wildest parts of your imagination on telling a story with a moral, and that keeps you on track.
So, what is a theme? It's your message. It's what you are trying to say, and what someone should go away from your comic with. The "Lord of the Rings" was that anyone can help, and that size is not important. Mine, Sex Percussions, is about that love comes in many forms, but it's important to love something. Dominic Deegan's is that things are rarely as they seem.
You can even change the theme for each story arc; Tales of the Questor seems to change each storyline. It started with "You can achieve anything" to "Anything can be overcome" to "Everyone has a message" to "Mothers are important", and the last arc was "Never leave friends behind." It looks like the next will involve paying for mistakes...
Just decide what it is that you would like to say, and go for it! State the theme as succinctly as you can, and constantly refer to it constantly. But...decide on what you think needs to be said, and let it guide you.
Oh, and just as important: Don't feel that it's necessary to have a theme! Some comics, especially comedy comics, don't have a theme. That's fine, too; just be entertaining!