that is a difficult question.. ghost in the shell is definitely one of them, but i also think cowboy bebop is really good, also tengen toppa gurren lagann, sidonia no kishi and aldnoah zero
ghost in the shell - because this is arguably the most philosophical anime i have ever watched and continue to watch
cowboy bebop - because of its very unique approach towards space travel, human over-expansion across the galaxy as well as its story around this concept
gurren lagann - because of its artstyle and absurd story and characters, the likes i have never before or since in anime history
sidonia no kishi - because of its very interesting portrayal of humanities last chance of survival inside a seed ship (a seed ship is a ship that is designed to have a very large population that eventually decreases until only 1 survives and was originally theorized to be used to go to planets that would take hundreds of years to reach) as well as its depiction of how the hygg's "god" particle which was very recently discovered by the Large Hadron Collider
aldnoah zero - because of how smart the main protagonist is and how humanity was portrayed as colonials vs indians except that earthlings are the indians.
i have yet to see an anime anywhere near as good as ghost in the shell, but i keep hoping :)
I would have to say either FullMetal Alchemist Brotherhood or Tokyo Ghoul, honestly. Those have the best plots, but the colors and drawings in Ouran High School Host club are plain breathtaking, and the soundtracks for Kuroshitsuji/Black Butler are definite earworms. Danganrompa was just really interesting to watch... it depends what category of 'best' you mean, but if you mean overall, FMAB, definetely.
Death Note is hands down my favorite anime. It is about a teenage boy who finds a supernatural notebook. Anyone whose name is written inside the notebook dies. The plot is intense and interesting, the songs are fantastic, and the art is just right. It also has likeable characters that I could relate to on certain levels, and best of all, there is no romance. I can't stand anime that involves romance.
Hokuto no Ken (original T. V. series, not the horrible film that tried to chop up an epic saga into a movie runtime, and not the Manga Entertainment bastardization where they omit a lot of storyline and put drum-n-bass music over it).