Demonomicon of Iggwilv: Yeenoghu
Creature Incarnations: Kobolds
Class Acts: Wizard
Ashen Covenant
Codex of Betrayal: Beleth
Backdrop: Cormyr
Wish Upon A Star
Ritually Speaking
Trapped!
The Bloodghost Syndicate
Mithrendain: Citadel of the Feywild
Ecology of the Genasi
Intelligent Items
Class Acts: Playing Swordmage
The Gladiator
The Pit: Running Gladiatorial Campaigns
Domains of Dread: Sunderheart, The Funeral City
Creature Incarnations: Gnolls
Demonomicon of Iggwilv: Baphomet
Playing Minotaurs
Bolded those that I really like (hope I didn't miss any)
EDIT: Ups, didn't notice it was a poll... sigh, I need new glasses
The list is great.
I would like to see others' lists of nominated articles! Maybe after a while I'll compile the nominated articles for a second poll.
It would be hard for me to narrow down my choices to fit 160 pages with the six or so issues out...choosing after 12 are out is going to be very very difficult. I don't envy the editor's job here.
So far, these are my favorites (no order)
Treasures of Ashardalon - themed article blending fluff and crunch
Playing Gnolls / Creature Incarnations: Gnolls / Demonomicon: Yeenoghu - these three complement each other really well (especially when I'm about to DM part 4 of H2: Thunderspire Mountain....no doubt this is not a coincidence

, and one of the benefits of Dragon going back In House at WotC)
Gladiatorial Fights / D&D Gladiators - this pair would be enough to start a campaign with, with new mechanics included.
Wish Upon a Star - this article was great. It gave solid story for a new take on the warlock, and backed it up with flavorful new powers.
In a way, I wish WotC could find a way to do themed books after a couple of years...something like a devoted Demonomicon of Iggwilv, or Ecologies type books (like Paizo's Ecologies).