I get asked this question from time to time, so I wrote up a "pat answer" to point to:
Dragons at Dawn focuses on Dave Arneson and the Minnesota group of gamers. It deliberately tries to build on the quirks and unique things happening there while excluding more familiar game elements - so there is a Merchant class and a Sage class, in D@D for example; the magic is alchemical, combat involves saving throws to avoid damage and so forth.
Dragons at Dawn also looks to a lot of the root elements found in Adventures in Fantasy that were present in early Blackmoor, the combat modifiers, and elven song magic, for example.
Dragons at Dawn is set up around a core game of two ability classes (warrior, wizard), in the basic game, to which everything else can be added or ignored without affecting play much.
Champions of ZED on the other hand, has none of that "experimental" or quirky stuff from Blackmoor and AiF. Wherever possible, CoZ hews as close as good play and the law will allow to a combined and collated version of the game information found in the 3lbb's, Beyond This Point Be Dragons, CHAINMAIL, the appropriate sections of the Fist Fantasy Campaign, Supplement II and Gygax and Arneson house rules and comments from interviews and web posts, etc. My efforts are to make the game what it was meant to be in informed compromise between Gygax and Arneson and nobody else. Hence, only two or three little bits from Greyhawk.
There are some points of agreement and crossover between CoZ and D@D of course, but those using Champions of ZED will generally find themselves in much more familiar D&D territory with interesting twists and turns they probably never heard of, whereas Dragons at Dawn is its own game entirely.