Note that in some states, doc fees are actually regulated - Maryland, I believe, limits "dealer fees" at under $100 (which means everybody has a $99 fee). You can negotiate around this if you're working with dealers in different states by negotiating the price of the car as "including everything but tax and tags". I had other dealers try to hide the destination fee separate from the MSRP then tack it on later and other shady ways to make it look like they were coming in lower below invoice.
Do your homework, don't expect to pay thousands below invoice, be firm but fair in your pricing requests, and don't let yourself get pushed around, and both you and the dealer can walk away happy.
EDIT: Also, you can get at least new GTIs below invoice even including doc/dealer fees, but realize they're popular cars and as such you're not going to have the dealer scraping pennies on the car. Also watch out for games - they may give you a killer deal on the new car, but destroy you on your trade in.
Also don't forget that they still make money on a car they sell below invoice - mostly via dealer holdback, although there are other volume promotions and the like. If they're willing to sell it, they're making money (or they're Pontiac, Saab, or Saturn and are just trying to liquidate
)