2006 List:
1. Revolutionary Girl Utena
2. El-Hazard
3. Tenchi (including Magical Project S)
4. Monster
5. Berserk
6. Ruroni Kenshin
7. The Vision of Escaflowne
8. The Big O
9. Sailor Moon
10. Slayers
2005 List
1. El-Hazard (tentatively)
2. Tenchi (including Magical Project S but not the two new series that I haven't seen yet)
3. Slayers
4. Revolutionary Girl Utena
5. Monster
6. Ruroni Kenshin (Seasons 1-2 and the 3 OAV episodes. I haven't watched the rest)
7. Noir
8. The Big O
9. Vision of Escaflowne
10. Sailor Moon
2004 List:
1. El-Hazard
2. Tenchi (including Magical Project S)
3. Slayers
4. Shingetsutan Tsukihime
5. Noir
6. Revolutionary Girl Utena
7. Kare Kano
8. Inu-Yasha
9. Ruroni Kenshin
10. Sailor Moon
Not a whole lot has changed from 2005, probably because I haven't watched much new anime this past year. Full Metal Alchemist and Full Metal Panic are on my list of series to watch eventually, and I hope to finish Azumanga Daioh, Kare Kano, and Inu-Yasha someday. All five of them could conceivably find a place on this list. Bleach exudes coolness up to a point but there was a precipitous drop in quality after the Soul Society arc, and I haven't picked the series up again.
Anyway, as for what did change, Revolutionary Girl Utena toppled El-Hazard from the #1 spot because of its thought-provoking and inspiring story. El-Hazard is great entertainment, but I find myself puzzling over and contemplating the characters and plot of Revolutionary Girl Utena more often. Berserk earned a place on the list for being such a starkly different and surprisingly intelligent series, while Noir dropped off of the list from lack of staying power, despite being great fun to watch. Sailor Moon manages to hang around probably from nostalgia and sentimental value (even after so many years I still find the Nephrite/Naru arc touching), and Slayers stays on the list because...well, maybe because it stars Lina Inverse and it's kind of hard for a human being to argue with a Dragon Slave?
Oh, and I happened to notice this...
13 Magical Project S
Woot! I applaud your great taste, Mr. What, although knowing you this probably has something to do with Pixy Misa being a mini-Mara of sorts.