We're super happy with our Toyota Matrix, which replaced a Jeep Liberty. This is the analysis I did to start our buying process:
https://docs.google.com/spreadsheet/ccc?key=0Ao1XSBz4nTP3dEVnT3ZTQm5qbnRfbld1NEpqaEdkMncFirst, I read the article on Mr Money about Smart Cars for Smart People and added all the cars to my spreadsheet. We were getting rid of a 2009 Liberty though, and I knew it would be a hard sell for my fiance to buy something older, so I didn't go back too terribly far in model year. A few years didn't have an overall ratings, but I left them based on overall reliability of the model. I just noticed I'm missing 2009/2010 Toyota Matrix/Pontiac Vibe, I have no explanation for this...
Next, I paid for a one month subscription to Consumer Reports. I plugged in the overall reliability ratings of all the cars. Note that only one model year of the Versa gets a 4/5, all the others are a 3. Our plan is to drive this car for 10+ years, 150k+ miles, so this is really important to me. I eliminated all the cars that did not rate a 4 or 5.
Third, I used Fuelly to get MPG ratings for all the remaining cars. Some didn't have enough users there for me to find the data reliable so I pulled from the EPA instead. I didn't keep track of which is which, but there doesn't seem to be a big difference honestly. If I hadn't been pressed for time I would have done city & highway, but I just stuck w/combined and eliminated everything below 27MPG.
Finally, I used Edmunds to look up the max. cargo space. I also used KBB (I'd use Edmunds if I did this again) to get the value for a car w/average miles for that model year. So, 2012 with 12,000 miles, 2011 with 24,000 miles, etc. This was more just to compare which models sold for a higher price than their "peers" than for actual negotiating w/dealerships or anything.
In the end, we got our Matrix with 26,000 miles for $13k. So far so good!
ETA: I never considered a Subaru because I knew we didn't want AWD and I knew they sold for higher prices than something comparable because of their popularity with the "crunchy" types. Also, all MPG is for automatic transmission w/the smallest engine, in 2WD model. Matrix did come in AWD for a few years, and also was sold w/a 2.4L engine as an option, watch out for those little details. Sometimes you have to pull the Carfax to see the engine size before you go to look at a car.
Finally, once I had all this analysis done, we went looking specifically for a Matrix. I invented a comparison ratio of price:miles as those were the two most important factors to us and we felt the price we paid made our car a superior value to other cars.
Oh, and my dad looked back home in our rural town for deals for me and we realized prices were significantly more. We decided that here in Chicago the dealers get by on low margin high volume. So, don't be afraid to travel a little for the best price.