So what would be a good price for a:

2009 Grand Touring
2007/2008 Grand Touring

assuming relatively low miles (<30000) and good condition. I figured that it would be best to either get the 2009 refresh with certain mechanical upgrades for reliability or a late first generation would be good because there will still be some years before the extended warranty expires.

I've looked up the trade-in and dealer prices from KBB, NADA, and Edmunds TMV for each year and found that Edmunds and NADA are close (within $1000 of each other) and KBB is pretty out there. Essentially I'm wondering if the NADA and Edmunds values accurate or not considering the relatively low supply (not as many later year models as there are 2004s and 05s), the fact that production has officially stopped, the abysmal fuel economy (I don't mind, but people buying cars these days care a lot about it, so that'll kill demand), and the fact that for a traditional sports car it has mediocre power and crappy torque (again, I personally don't care, but those issues will kill demand within the buying population).

The base pricing (without considering miles and condition) in model year order (07,08,09) from the three sources are:

NADA: 13000, 16400, 18400 (Trade in); 16200,19750,2200 (Dealer)
Edmunds: 13700,16340,18750 (trade in); 16100,20150,23000 (Dealer)
KBB: 15500,18000,21200 (trade in); 19700,22100,25500 (dealer)

 

To simply answer your question,

Somewhere between trade in value and dealer retail is a fair value.

The closer you are to trade in value, the better the deal is for you.
The closer you are to dealer retail, the better the deal is for the dealer.

You decide which side of that scale you would rather buy a car at.

BC.

 

Research prices in your area. Look at your local classifieds, craigslist, auto trader, and cars.com. Edmunds and KBB aren't all that relevant compared to actual selling prices.