The Prius deserves to be on every magazine's best car list. It may not be the definitive wave of the future, but it's a terrific start. The latest revision has lots of interior room, uses clever solutions like a tall cabin, and of course is a hybrid. To ignore a car such as this in a best car list would be myopic.
The Focus in theory is the most advanced car Ford make worldwide (remember, warranty issues are not a consideration in this argument, and EU Focii have a far better rep than US cars so clearly origin matters too -- the design can be made sound is my point). Ages ahead of the Escort, Mondeo/Contour, Sierra/Merkur or any other global Ford offering.
Cars that don't belong on that list IMO:
The Mazda RX8. Wankel for the sake of being different in the 21st century? Although they look better than ever on paper, Wankels are just not on, sorry. NSU knew best three decades ago (or if they didn't the market taught them; they folded into VAG...). Why Mazda have not caught on yet is anyone's guess.
Chevy Corvette. Boorish styling basically unchanged since the 80s, chest-wig charriot IMO, major revision coming soon, why not wait and judge the new car?
Acura TSX and Honda Accord. Pick one. Both seem competent sedans and ought be be built very well. Why have both on the list -- doesn't the advertising money come from a single source anyway? Do they pay double?
More thoughts: I'm glad the G35 is on there, Japan or someone needed to make a BMW 6 series for years now since BMW had stopped (though they are resuming, which will probably make the G35 redundant IMO). The Nissan cousin, the Z, looks terrific except for one detail: it seems like they forgot to give it door handles, then grafted them on at the last minute. I can't deal with the door handles - silver, prominent, apparently tacked on as an afterthought. I've often wondered if one could use G35 doors on a Z! The rest of the car is very graceful, almost like 1930s aero designs. Shame.