Well, this is my first full year of watching anime and I spent allot of the year digging through the library of a streaming site. Consequently most of the titles i watched aren't actually from '09. After browsing the forums here I realize I've probably missed a good portion of the better shows of the last few years. However of the ~35 shows I did watch some of the best were:
Last Exile - A great story with an fantastic setting. Something about the flying battleships just captures my imagination. Best of all, I can share it with my sisters without reservation.
Hayate no Gotoku seasons 1 & 2 - Nothing beats 1/2 hour of laughs after a long days work. Very little is serious in this show and it's great.
Code Geass 1 & 2 - Sure it had it's faults and I understand that there are better shows out there that I haven't seen yet, but it had me hooked at the first cliffhanger and drug me though until the last episode of R2.
Aria - Not sure why I like this show so much, nothing ever happens. Still it's a very beautiful show and I keep watching.
Melancholy of Haruhi Suzumiya 1 & 2 - I watched the first season in original broadcast order and nearly dropped it on the first episode. However, I was tired and any show with the audacity to air the episodes out of order deserves a second chance. Haruhi's outrageous personality, Kyon's deadpan narrative, and the whole off the wall premise kept me entertained until the Endless Eight... I found some translations of the light novels and I can't wait for Disappearance in '10.
Spice and Wolf 1 & 2 - Personally, the best of the year. The art work, the setting, the central theme, the business dealings, Lawrence and Holo's relationship; it all works for me. One of the few times I've cared about the characters enough to want to give them advice. I'm really hoping for a season 3. Even if wiser minds in the Spice and Wolf thread suggest it's unlikely.
Heroic Age - A good, clean space epic made better by the fact I watching mostly mediocre shows at the time.
Those are the one that stand out the most anyway.