which size class? Are you looking between an Accord, a Camry or an Altima? A Sentra (boo), corolla (yes!) or civic?
Lets look at it this way... The Accord has proven reliability and driveability. It is consistently a car and driver "Ten Best" winner BUT so many other manufacturers have proven their reliability and "fun to drive" factor.
Go test drive a Camry. It's a couch on wheels and I don't mean that in a good way. Its handling is not as taut as all cars in its class. the fit and finish of the interior (no haters please, this is true) is less impressive. It's expensive, a snooze and is more invisible than the over-rated honda accord.
The Altima offers a powerful and reliable 2.5 liter 4 cylinder or v-6 both standard (2010 models) with a continuously variable transmission (CVT) for the best possible fuel economy and performance.
I have to be honest, I only like TWO toyota's and I will tell you which and why: The Corolla for its affordability, reliability and SUPERIOR gas mileage. They are rated at 35mpg highway and are just super smooth for it's size class... The only downside would be less power than available in other similar cars, extra cost safety options which should be standard and thirdly, lesser breaking than all other models in it's class (per caranddriver.com) Secondly, the Prius, as it's the best hybrid system out there. Bar-none.
In general, I can't give you an answer as to which one is the overall best becasue there are so many good cars out there besides the japanese. I am not one to rule out other cars such as Hyundai (extremely reliable cars and a great value for the money/warranty) Ford or Chevrolet. Considering only japanese automakers is a stereotype that was true in the 80's, not now.
If you want more specific details, just edit your question and I will tell you what you want!
Good luck,
Tyler