FLCL actually has substance, in which it differs from many of the other "nonsense" shows. There is a plot, and though it might not be very coherent, it does string along.
I love the visuals, and i love the culture references, which were often from a generation removed from the usual audience, but still worked. Crystal Pepsi? They stopped making that when I was about 8.
I like Amarao most of all, especially in the John Woo tribute episode "...I'm not a kid any more: I can buy my own insurance and everything!" I actually like the dub of this show, and in fact have never seen it in Japanese, as I see no need, so entertaining are the voices in English.
There has almost always been a year between the times I watch this(its hard to imagine this has been out for 6 years), and each time, a new layer of meaning un-peels for me, like some sort of weird and delicious fruit.