Often, an anime is a condensed but basically faithful re-telling of the manga on which its based with an ending made up for it, but FLCL is not. Manga-FLCL (hereafter 'FLCL') has the characters of anime-FLCL (hereafter 'Furi Kuri') and the same basic idea, but are otherwise completely different. About the only other thing that makes them the same is how short they are: Two volumes of FLCL, six episodes of Furi Kuri. Leaves you wanting more but realising they were exactly as long as they needed to be.
The concept behind the manga, or maybe just Naota, the main character, is of suddenly going from watching the people in the asylum to being the epicentre of insanity. The setting, Mabase, is filled with weirdness yet most people don't worry about it. They've come to accept it and in a way become part of it. After all, nothing emphasises strangeness to one person's perspective more than the masses not recognizing it, right? The anime explores this aspect further, but that's another review. But more than that, its about pre-teenage angst, loving the wrong girls (which is redundant), relating to family and robot substitute brothers.
The pace moves like a squirrel. Sometimes its just kind of sitting there, sometimes its frantically running for it's life, and sometimes it goes somewhere it seems to hope you can't follow it. Either I read too much into things, or FLCL is rife with metaphors and things that I just didn't get or see the first time through. Luckily, its a damn fine read so going back through it isn't exactly a chore. Its kind of like looking into the mind of an insane genius.
What adds to the confusion and the overall cool of the story is the art style, which is almost sketch-like, but detailed at the same time. Some of the art is way too crowded, but usually in a way that helps right until you try to read the text. The story is odd and at times random, but always enjoyable and engrossing. If you know the anime first, FLCL will seem a little "off", but give it a chance and you'll come to appreciate the more varied pacing and new looks at the characters.
I do prefer than anime, though, for the obvious reasons. First and foremost, the pillows lay down an outstanding soundtrack and if you have a friend in Japan, offer them whatever they want to buy a copy for you. Also, animation makes it easier to tell what's going on. Still, FLCL is worthy of being it's own entity, and of being read and enjoyed on it's own merits.
All in all, an excellent manga. Of course it is: its GAINAX!
Other than a complete as of several years ago list of TokyoPop manga and art books, none.