1. Higoroshi no Naku Koro ni (and Kai)
This anime is pretty much the top of its genre and for good reason. The chilling atmosphere of Hinamizawa at night, the background noise of the cicadas chirping at the extremely well executed horror and gore scenes. The intricate story line, amazing characters and unique premise only propel an already great anime to even greater heights. This is without a doubt my favourite anime of all time.
2. Kokoro Connect
The characters, the premise and the feelz. These three integral aspects of what is possibly one of the most unique anime I have ever seen are pulled of exceptionally well. The funny moments made me laugh hysterically and the sad moments made me wish you could hug a fictional character.
This anime's truly strongest point though is its characters. Each of them has a surprising amount of depth given to them (except maybe Aoki but he is still developed and interesting) considering the small number of episodes compared to most live action dramas and each have interesting and well thought out strengths and flaws. The characters are relatable, the voice acting fits them perfectly and each character adds an amazing element to an already intriguing premise.
3. Death Note
L and Light (N to a degree) are some of the most interesting characters I have seen. This anime has the most complex plot, good characters and a very interesting premise but it is the suspense incorporated into the complex plot that make it amazing. I was always itching to see who would come out on top and how they would do it.
4. Elfen Lied
Honestly, if the gore and nudity bother you that's fine but I find it hard to believe people don't acknowledge this as a master piece. The story is both touching and horrific and it is certainly captivating with a unique premise serving as the centre piece for everything.. and then there is Lilium.
Oh my God Lilium . (May contain nudity, I didn't check. Watch at own risk.)
5. Puella Magi Madoka Magica
In the end this had to be the fifth spot. I love how it appears as though it will be one thing at first and turns out to be such a twisted and sad story. The artwork - especially on the witches - is amazing and the plot twists and over all story kept me begging for more.
This is a pretty rough list, my top five are definitely these anime but the order tends to change.
Honourable mentions
Naruto Shippeden - It's a shounen anime, and those are not typically known for having complex plots or backstories nor good characters but this is not the case here. Naruto Shippuden has great action sequences, really knows how to push those emotional moments (although not always to the levels of some of the above anime), has a really developed story and has some truly fantastic characters such Shikamaru, Hinata, Itatchi, Jiraiya or even the main man himself.
Azumanga Daioh - It's just so funny. I used to think I would never watch a slice of life an anime and I am not entirely sure how I ended up watching this but I'm glad that I did. There's pretty much no plot, which is typical of the genre, but the characters are amazing and when things are funny, hey truly do make you laugh. Osaka is probably the most amusing character ever.