OK, here is my list of five in alphabetical order, and the obligatory disclaimer: the thread title says "favorite series" so the selection is based on my own personal enjoyment, not a critical or technical rating of each show.
- Bokura ga Ita - This is not your typical high school romance. There are no real heros, villains, or perfect individuals, but a cast of very believeable characters with flaws and problems that will ring true for most people and provide lots of emotional ups and downs. Plus Nana-chan's voice simply induces melting.
- Kanon 2006 - Great animation and a gripping story. Just about the only series running right now that I have to watch the instant the download is complete.
- Ouran Koukou Host Club - I still cannot believe that I ever got past the yaoi-istic OP when I watched the first episode. This series was hysterically funny, with biting satire and some wicked parodies, but it also boasted some serious themes and presented some scenes that were quite capable of putting a lump in my throat.
- Suzumiya Haruhi no Yuuutsu - The number one criticism of SHnY seems to be that it can't be that good because some people like it too much.
Interesting theory. I'm kind of pissed at Santa though: I only had one thing on my Christmas list this year, but there wasn't a Living Humanoid Interface under the tree. 
- Utawarerumono - Hardly a masterpiece, but it had an interesting story, good characters and was a very fun ride overall.
And honorable mentions for two shows that I really wish I could have included on the first list: