Dictator: TTGL is overall a good anime I just did not like the ending at all it was down right depressing. After all the crap that Simon and his friends went through they deserve a happy ending. I have never been a big fan of sad endings or sad animes in general and never will.
Monster, easily. The rest I kind of have to ignore a few things for example Boogie Woogie Feng Shui is an awful episode of Cowboy Bebop but as a whole I'd consider it a masterpiece. Most episodes of Mushishi are masterpieces, Wolf's Rain's a masterpiece if you can ignore those pointless recap episodes. HxH 2011 is one during the Chimera Ant & Yorknew arcs. Ping Pong the Animation is one too, easily. That's it, due to most of my other favorites including a more glaring flaw. LotGH seems like it's one but I haven't watched the 110 episode OVA yet, just the movies set before/during it (one was set prior to the series, the other one, Overture, was episode 1 & 2 but better [heard from one of my friends on MAL]).
The first thing that comes to mind is binan chikyuu bouei-bu love(Cute High Earth Defense Club Love!) it's just so perfect! especially the last episode, it makes more sense than anything I've ever watched before.
All anime has flaws, like Cowboy bebop which I personally find a overrated,especially with the last two episode being a repeat of a better episode despite important dead, making the episode underwhelming.
If I have to pick one, I have to go with FMA Brotherhood. Granted I do feel like it is somewhat too shonen at time, trying to show how pure and innocent Edward really is, which sometime sicken me, but a bit, and overall is damn near perfect, but not my personal favorite. My favorite by the way is DBZ, which has a huge flaw call the Buu saga.
Also my other anime that I consider a masterpiece is Hellsling Ultimate. It does it job perfectly, the action, the atmosphere, great animation, voice acting, everything. I guess the ending got a bit confusing, but again no anime is perfect, but Hellsling Ultimate is close enough.
Also Queen Blade, because oppai, lots and lots of it lol, which come to the reason why I don't thinkCode Geass is a master piece either, useless fan service. It is my second favorite anime, and at some point was my favorite, but I can never understand why it try to have fan service when it seem out of place. Also season two just became who had the better robot, instead of strategy. Season 1 was a master piece, but the second season had enough flaws to make it hard to say it is a masterpiece.