As in any other good comic, have well thought out story line, begging, climax and concrete end.
Be sure to make your panels logical and have good pacing. Make sure that word bubbles and illustrations indicate the page flow and make it easier to follow.
Honestly, I've started so many comics and never saw them through for a few reasons.
Good lord, Cat-theBat, are you me?
Anyways, Animangel, as with any other type of comic, a good web comic must serve one basic purpose: telling a story or a joke, or some other sort of narrative. Even one-panel strips (a la The Far Side) do this, albeit with a single gag joke, and in a single hilarious panel.
Like its parent art form (writing), if the story is not well thought-out and meaningful, or the joke isn't funny, the comic just isn't going to be that appetising. I could create the most beautiful, most gorgeous visual art work in the world, spending thousands upon thousands on visual effects, amazing graphics, and masterful character design...but without meaningful character development, believable characters and plot, and an engaging storyline, my comic will still get horrible reviews, simply because its purpose was not fulfilled.
(Michael Bay, you had better be taking notes.)
Also, if you want to take a look, here's my web comic. Maybe it can give you some ideas.