I see my favorite anime in groups of clusters rather than individual shows, so I sort of cheat around with the question.
1) Yu Yu Hakusho / Rurouni Kenshin - personal bias, being my first 'real' animes, but they really had interesting characters. Yusuke was the definition of cool, while Kenshin was the humble killing machine.
2) Cowboy Bebop / Samurai Champloo - some say it is overrated, and parts of it do feel slow, but overall it has a really nice, kicked back relaxed filling. I bump it w/ Samurai Champloo because both are by same creator and generally have a similar feeling associated with them.
3) Death Note / Code Geass - The best strategy animes I have watched. I can watch them multiple times and not get tried, but the first time was indeed the best. Leave an impact on you for a while. But their story-lines being so awesome and far-fetched makes them contain certain parts that don't cater to my individual liking, but these rankings are really subjective, can very well be number 1.
4) Eden of the East / Angel Beats - I watched both these animes when I was feeling down / bored on life. Both have a positive vibe, go out change the world type of feeling (especially the former). Both left me really happy and positive after finishing. Short series so can't rank them as being the best, but definitely worthy for a top list.
5) Ghost Hunt - A random rare find I came across. I didn't think I would like it as much I as I did, but I really did enjoy it, and it remains a personal favorite.
Lots of other contenders:
Hunter x Hunter (cluster 1), Steins;gate (most likely cluster 5), Monster (would probably need it's own cluster), Detective Conan(possibly cluster 5), FMA / FMA B (own cluster probably), etc. At the moment, the cluster I chose is my favorite.