I did do some total cost of ownership type calculations, using the fuel economy figures from Consumer Reports and fueleconomy.gov and the "True Market Values" from edmunds.com.
I compared a 2000 Rav4, a couple variations on the 2005 Matrix, and 2003-2005 Priuss.
If i expect to have the new car 5 years or less the 2000 Rav4 actually comes out ahead, despite the worse gas mileage. From 6 years on both the Matrix and the 2003 Prius become cheaper than the Rav4, with the 2003 Prius a little cheaper than the Matrix. At 8 years the 2004 Prius becomes cheaper than the Matrix and at 10 years the 2005 Prius becomes cheaper than the Matrix.
The downside is that according to both Consumer Reports and JD Powers the Prius saw a big improvement in reliability between 2003 and 2005, which makes getting a 2003 or 2004 Prius a little risky. And i had my first car for 4 years and my second car for a little over 7 years, so counting on making up the cost of the 2005 Prius over 10 years would definitely be stretching things.