I think Kirby confused me the most because it doesn't show what happens next in some episodes.

Paranoia Agent made my head spin. All I could figure out was a kid wearing skates going around beating people with a golden bat. I stopped watching it after episode 5. Higurashi also confused me a lot, too. In about every other episode, they all die then, next thing I knew, they were all alive and happy. Creepy. I never understood everything until I read one of the manga that goes along with the anime. As it turns out, every other episode is in a different world. In each world, someone goes mad with a suspicion and kills everyone else. I love the manga, but I can't watch the anime anymore. I just scares me way too much.

Most confusing anime I had ever seen would be 'Desert Punk' because of  the plot was so confusing and frustrating to understand. I mean the main character switches sides over and over and that confused me for instance in one of the episodes something happens to Punk then for the next two to three episodes the main character is his apprentice and had even taken on her own apprentice and goes through the process of training the apprentice the way she was trained but then it gets even more confusing and crazy. I don't want to spoil it for anyone that plans on watching it but it also has some crude and perverted humor towards inappropriate things.

paranoia agent was confusing by the time i got bored with it i didnt know WHAT was going on =.= but then again i found death note a bit troublesome after i got into the late episodes

I only watch the simpler animes, but the most confusing one I've seen is err I dont even remember the name...

Speaking tactically, Death Note really screwed my brain up. Bad. Code Geass's tactics really messed with me too. 
The weirdest anime I have ever watched was probably The Melancholy of Haruhi Suzumiya. Just... weird.
I enjoyed all of them though. 

chasrad : I agree FLCL is a really confusing anime series doesn't have only like 5 episodes or something?

I have to say Gag Manga Biyor. Mostly because of this video http://www.youtube.com/watch?v=2twxVgQPM6A&feature=related

I haven't seen that many that really confused me, the one that came closest though was Higurashi

Higurashi isn't all that confusing. At least, for me it isn't. I think the most confusing anime is FLCL. Seriously, Rev up that... electric bass guitar? What? Wait, now it's a shotgun. And that guy just sprouted a guitar slingshot from his head WHAT? HOW MANY ARMS DOES THIS THING HAVE? WHAT IS THIS I DON'T EVEN!?!?!

I would have to say for some reason I was confused by Full Metal Alchemist. Then once I got to the end of the series I was not confused anymore. I think that there is just a phase in the center where you have no idea what is going on.

I don't watch anime shows a lot but the one show I thought was confusing was FLCL on adult swim

The most confusing anime I have ever watch is Bobobo-bo Bo-bobo, even the name is confusing because it seems to not have any significance what so ever and I know it probably is specific for the Japanese, humor wise, because it was animated in Japan. But c'mon at least have a story or a plot throughout the series. Well it was a weird anime, but I like anime regardless. XD

I think that the most confusing anime I can think of is a tie between Higurashi no naku koro ni and FLCL. Higurashi for me was a confusing mystery that eventually sort of made sense looking back on it. It's one you have to watch twice to understand everything that happened. FLCL will never make sense in a typical way, no matter how many times you watch it, but that I think is the allure of it. It opens itself to so many different interpretations that you can put whatever you want onto it.

Evangelion was one for me. For most of the series it was fine. Each episode followed one another smoothly and combat eps were sometimes prepped in the previous one. THEN comes the last two or three episodes. Out of nowhere it's different. That was a WTF moment for me. It was completely unexpected and the last episode left me wonder what the hell had happened. Nothing made sense. All I knew was that it was inside Shinji's mind and I vaguely realized the 3rd or 4th impact had occured I had to ask my friend who had seen the other parts of the series to get an idea. I had a grasp on it, but it wasn't until Japan released the other half of the series to the US that everything finally made sense.

Excel Saga was another friggin strange one. Crazy. That show is just messed up. You don't know if the story is progressing or not (if there even is one) and the dialogue seems random. In actuality, much of the dialogue they say is really making fun of Japanese culture. So unless you know a good bit about Japan culture you'll never know what the hell is going on. Ever.

I'll go with FLCL just because of the memories (THEY BURRRN). I've watched GITS and it feels like my mind melts most of the time.

Maybe Monsters since the story is a more on a mysterious side that's begins when A family is killed by a murderer leaving  the Girl the only one shaking in fear  And the boy survive miracously by having a bullet lodge into his head.Years went by as both is taking care of  by separates family .Johann grew up into a killer and murdered his sisters new family .Nina discovered it was her younger brother is the killer and went to search for him to settle it but he's always on the move  killing everyone she's knows.So the real Killer is actually Nina since she was an expirement.As a child she managed to escape that Experiment since the director drugged everyone there>She fled home and told Johann all of those awful stories that happened there..Johann Spiro out of control and managed to kill there biological parents with the gun and force Nina to shoot him in the head to end the game.There's more to tell you but you have to watch the whole story from the ground up on Manga.com The rest is far to confusing to tell.

Neon Genesis Evangelion. The last two episodes. It's a good show, but shinji's way too messed up in the head. End of Evangelion totally takes the whole mindscrewness of the show from cryptic to the equivalent of taking lsd while schizophrenic. Hopefully the rebuild films will have a less disturbing ending.

billythekidmonster : In Hugarashi they just reuse the same characters rather then to move on with a new cass it's nothing but a parallel universe