Simple, go to a dealership that doesn't charge documentation fees. My local Ford dealer doesn't charge them...hell they even got my new plates/tags on the house for me.
That might be tough to find but...otherwise just use it as a I want 125 off the price of my car kinda thing.
Today, with the recession hitting the car industry hard, it's probably imposssible to find a dealer that doesn't try to stick you with some extra fees. From what I've read it's getting worse, since car manufacturers are narrowing dealer profit margins.
Yes, I did use the $125. doc fee as a bargaining tool on the total price of the car. Most dealerships wait until they get you to the finance manager before they spring the extra fees on you. Demand that the salesperson gives you the total "out the door" price before you settle on a price. If he/she will not, walk.
My car was Nissan pre-certified, which means it comes with a 84 month/100,000 mile warranty, but the finance manager still tried to sell me an extended warranty insisting it wasn't pre-certified, until I showed him their internet ad stating it was.
Here's a few helpful sites on what fees you should pay:
The list of state fees are as of 10-08 and may have since changed. Click on your state's department of transportation link to get the latest fees.
Some states' sales tax differs from their car tax, i.e., in WV the sales tax is 6% and the car (they call it a priviledge tax) tax is 5%; and besides registration fees, most states also have title fees.
http://www.edmunds.com/advice/buying/articles/117494/article.html
http://www.carbuyingtips.com/car3.htm
You've probably heard or read it already. Before you buy either a new or used car, research, research, research.
Gather all your info in a folder and bring the folder with you to the dealer. The folder sends a signal to the car salesperson that you are prepared to do battle.
Also read these 2 articles. It's a look from the other side.
http://www.edmunds.com/advice/buying/articles/42962/article.html
http://www.edmunds.com/advice/buying/articles/125308/article.html