I think my all time favorite issue was Dragon 313, there were just sooooo many gems in that issue from BORN OF DEATH, STRANGE BEDFELLOWS, GHOST ELVES, well now thqt I think about it I've probably used every article in that magazine, a true classic.
I also really loved 310, 311, and 312. The variant classes were excellent, and I have used them quite a bit over the past few years so I'd have to put them into my top 10.
Dragon 318 gets a nod from me aswell. I loved the OA 3.5 update. The isse also had pirates, and dinosaurs; it was kinda a Savage Tides precursor.
Dragon 315 the first campaign classics issue was Awesome. It might be the only issue I have used more than 315!.
Dragon 319 the Dark Sun issue was sweet. It also boasted the second half of the Greyhawk Regional feats, and the Cannibal Plague.
Dragon #298 the Drow issue was really well done. Great PrC, Vault of the Drow overview, and Flesh for Lolth...SWEET.
Finally, Dragon 290 and 291. Paul Kidd Fiction, and the Death Knights of Greyhawk what more could you ask for?