Things are quite even between them. nVidia provides the best balance between price and power in the high end, with the aforementioned 8800GT. ATI rules the roost right now, thanks to the Radeon 3870X2, but that's very pricy, and it's not really recommended anyway, unless you have tons of money. It also uses some "black magic" to achieve the highest performance in the single-card field
Anyway, considering your budget, I give you the same advice that I gave to wreckedcarzz: Buy a Radeon 3850. It's an excellent card for the mid-end, quite powerful to run without problems the most advanced games, but very affordable as well. If you can spend more money, it's either the 3870 or the 8800GT, both are good options, although nVidia has the edge in this case. It used to be a price difference between them favorable to ATI, but that does not seems to be the case anymore.
One caveat though: If you're going to buy the computer now (in two weeks, for example), my recommendation still applies. If you're planning to get the machine in a month, then wait a bit more. nVidia is releasing a new line of cards in March-April, and Intel is going to update the entire Core 2 line by then as well (note that the new Core 2 Duos are available, though not in great quantities). So you may have to revise your choice of the Q6600 by then.
Ooops! Brandon finished faster than me
. So, what nVidia cards you used to give you so bad results? Reading "uses system RAM for graphic purposes" reminds of that wonderful card, the 6200 Turbo Cache, the king of the hill