I watch a ridiculous amount of anime. like.... RIDICULOUS. Like you're reading this right now and thinking "oh he is exaggerating" but I'm not. I have a 500 gb external hard drive that is literally FULL. of nothing but anime. plus I own all the miyazaki movies (almost) and 5 seasons of bleach and the Elfen Lied Complete collection *pauses for breath* and the NGE platinum collection and Eureka Seven seasons 1, 2, and Good Night, Sleep tight young lovers. And more soon.
That being said I find it extremely difficult to pick a favorite. So I'll list some that I really liked but are maybe a little less well known.
RahXephon - a beautiful testament to Evangelion. At first it seems to be the same story and premise, but over the course of the series, grows into its own incredible masterpiece.
Romeo X Juliet - Maybe I'm biased because I love Shakespeare, but this gorgeous Sci-Fi adaption of the original love story really touched me.
Noein - I had a hard time finding background info on this one, but I really liked the concept. It fully explained to me the entire theory of parallel universes, and the animation style was new and different, and I quite liked it.
And many many many many more. If you check out my youtube channel, I plan to do an Anime Recommendation every time I post a battle video ;)
P.S. My opinion on Naruto/Bleach/other tedious long super popular anime: I like the stories and the characters and the concepts. It's not the creator's fault, per se, that it got super famous yet bastardized in the transition to anime. Adapations from Manga are often, in my opinion, disappointing and poorly done. I have however watched all of Naruto (no shippudden yet, I'm reading it though) and I own Bleach up through season 5. It just makes me sad that they couldn't do a better job in the animated rendition of what was clearly such a great idea. Kind of like The Last Airbender movie. God, I cried afterward I was so upset at its shittiness. anyway yeah the manga's great and the anime sucks. especially filler seasons jeez they are SO BORING
but I watch them all anyway