The Nook Color is still $250 new (though you can get down to around $150 on ebay i believe), plus it's hardware isn't as updated as the Kindle Fire
The Nook Color has a 800MHz processor, the Kindle Fire will have a 1.2GHz dual core processor
The Kindle Fire has a high quality IPS LCD Display, the Nook Color just has an average LCD
The Kindle Fire is running on Gingerbread (2.3) while the Nook Color is on Froyo (2.2). Yes, the Nook Color can be hacked onto a different version, but the same will probably also be true of the kindle fire.
The Kindle Fire has the Android App Store out of the box, which has many more apps than the Nook Color's Appstore. The Kindle Fire probably will get the Android market when hacked, Nook Color can already get it.
The Kindle Fire is lighter and smaller than the Nook Color.
The Kindle Fire will have the Silk browser, which should make for a much better browser (look it up).
The only thing that is better on the Nook Color is that it has a MicroSD slot while the Kindle Fire won't.