All of them are confusing.
Akira with its 30min long ending (it may have been longer. I can not remember. I fell asleep before they wrapped it up. Everytime.)
Ghost in the shell movie 1 with its cliffhanger ending.
Maccross (T.V. Series) with its cliffhanger ending of taking the "S.D.F.1" back into battle after it was retired.
And anything else they have.
Some of the times the confusion is cool like plot twists and things of that nature.
Other times it is just wild Plot turns that do not add up. (Dragon Ball Z movie: Goku Vs Lord-Slug.) Many of them are cool like the Dragon Ball One I mentioned.
Others are Lame. So lame you have to rewatch a few shows just to justify what you liked the first time. When I see the lame stuff I stop watching and forget about the rest of the show or franchise.

To answer the question though ... all of them are confusing.
It is one of the things that keeps me hooked on "Anime" well after my teen years. (Granted I am more selective now. But still, Anime is an art form I do not wish to die-out anytime soon.)

Good Luck To All.
I'm done. Stick a fork in me.
Peace.

FLCL...MIND F*** x 1 000 000...

DBDonald : it was DBZ it started with goku being so strong i like anime with people growing stronger instead of being strong

Man, I need to see Evangelion.

Here's one. King of Thorn. This anime we'll really mess with your head.

FLCL is another one, but I definitely understood it more than King of Thorn. FLCL also a fantastic charm that no other anime can match.

Pokemon made no sense at all what do they do offair?Why is there no bathrooms?What does it feel like to live  inside a pokeball?If there is one thing they did make sense in the series it is water pokemon not being able to battle on land but the game was the complete opposite.

I wholly agree with everyone who said FLCL and Paranoia Agent.

FLCL was bizarre both in its plot and its animation style which regularly switched from anime style to manga frame style. And one of the previous posters pretty well summed it up with "alien woman wants to molest young boy". It may also be worth including "she turned his dad into her personal slave".

As for Paranoia agent... let's just say Satoshi Kon had a strange, strange mind. Everyone who liked the Mind-F@!# of Paranoia Agent should check out his other works:

"Paprika" : Technology that allows one to enter other's dreams seems responsible for people randomly going crazy and killing themselves. Is it actually possible to trap someone in a "dream state" while they retain consciousness?

"Perfect Blue" : A pop idol turned actress is increasingly stressed by the roles she must play to attain worth as an actress. But that's nothing compared to her stalker problem.

"Tokyo Godfathers" : Three bums find a baby abandoned in a dumpster on Christmas Eve.... nuff said. Some people might think it's a chick flick, but those people should be directed to the next anime in line.

"Millennium Actress" : A TV interviewer and his camera man enter the memories of a famous actress as she relives her past. It's definitely a chick flick.

KlawedFlaw : Nail on the head. "Garzy's Wing" is the most confusing anime I've ever seen.

What I don't understand is why so many people are confused by "Higurashi no Naku Koro ni."  Rika is forced to relive the same agonizing death and rebirth cycle due to the face that she is the vessel for the God that causes the illness in village. It's kind of her curse. She when people live in the village for a certain amount of time they fall under the "Hinamazawa Curse," which manifests when the person attempts to leave the village. They become irrationally violet, hence why Rena went on her school massacre. Rika is the reason this curse exists and why people in the village are safe from it. 

I'd explain more but then I'd really be spoiling it but watch the second and third season of "Higurashi" if you're confused. I promise it will make sense.

Anyone ever see "Doomed Megalopolis"?
That show confused me to no end. (I know I already answered. I felt like answering again.)

I am not certain if the stuff I did not understand was cultural differences or story, plot, and writing taste. (It took a week for my "U.P.N.1" channel to air that thing episodically.)

Granted I was just a kid when I saw it but the whole story seemed to boggle my mind. The Part that sticks out the most is the ending. (Overwhelmingly brilliant and simple.)

And that's the rub.

When it got to the end everyone expected a Spectacular, Over Abundant, Pay off.
What we got instead was something that "Nuked your soul". Or gave a person a head ache.

I was one for the head ache category.

Similar thing for the "Tank Police" Movie Ending. (Though I will defend the "Tank Police" Show to no end due to the comedy alone. It's very funny for me. Even still to this day.)

Thanks for the chance to go back in time with my memories.
Good Luck.

Good Luck To All.
I'm done. Stick a fork in me.
peace.
http://www.youtube.com/watch?v=BqauJCsIRYs

Belinni : I agree...Higurashi would be my answer too.
The constant 'restarts' not only confused me, but completely turned me off to the show and I never bothered to watch it to the end.

Does Lucky Star have a plot? Or is it just a sitcom? Just saying, I've seen many clips and a bit of the first episode, but no matter how much I see, I can't figure out whether or not all the diet problems and facepalms and all-nighters and bathing and showering together has any point.

bobobo-bo bo-bobo is awesome, but it is really confusing, but it if a funny one!

I admit, I've seen a decent amount of Anime but in no respect a lot, The most confusing, Well... It's really not so confusing as it is trippy but FLCL is the most confusing anime I've seen, Mainly due to a specific few scenes. But I'm sure there is much worse out there.

FLCL hands down and I'm glad I'm not the only one that didn't understand that anime, after I re-watched a few times I still sat staring at the screen thinking WTF did I just watch that just didn't make sense at all.

The most confusing one I have ever seen is Naruto. I did not watch a lot but I know its complicated. I researched it on the internet and let me tell you, it is complicated. Enjoy your day.

To me it would be FLCL.

vanelan : You should really watch Higurashi til the end! It may be confusing but you will get all the answers in the second season, it's one of my favorite animes actually! In the end it actually makes sense!
The most confusing anime I've ever watched must be FLCL I didn't understand a thing but it still was awesome! ^__^

Although I love it to death Fooly Cooly still confuses me a bit.

BUT... speaking of confusing animes, anyone ever see Bobobo-bo Bo-bobo? that show defines confusion, I dare you to make sense of their stories.