I did an analysis 18 months ago when we replaced our Jeep with a Matrix. My spreadsheet is a little out of date, but you might still find it useful. This was my methodology
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Good luck!
https://docs.google.com/spreadsheet/ccc?key=0Ao1XSBz4nTP3dEVnT3ZTQm5qbnRfbld1NEpqaEdkMnc&usp=sharing
mlipps has great advice imo!
also, last time we got a car, Edwards dot com had decent life-of-vehicle cost estimates (including maintenance, insurance & depreciation in addition to gas).
Definitely test drive your finalists - a *real* test drive, not just around the block - hard acceleration vs. soft (with any mpg stats monitored); aggressive downshifting & braking, up & down hills, cornering, parking/backing up, merging on highway, stop & go, etc - can easily fit all this in a 10 or 15 minute stretch but the salesperson might be surprised, apparently most folks choose 'around the block'.
If you do get a new car, once you decide on the make & model you can do an aggressive internet search to find what you want at the best $, usually your local dealer can either match or actually get you that exact car by swapping with the other dealer if it's within a given distance (depends on dealer, but up to 500 miles is possible)
We have a Mazda 3 hatchback and love it. Manual skyactiv transmission (this is our second M3 hatchback, our first didn't have skyactiv so was much lower mpg). Our mpg is low-mid 30s in town and high30s-low40s highway. Easy on acceleration and you could beat those stats; hypermile and you could likely obliterate them! If you don't care about "sporty", this may be more engine than you need, could get even better mileage or lower purchase price with a different car.
Likes: great gas mileage, great "drive" feel, roomy (plenty of back seat leg room vs. many hatch's, w/all seats but driver folded can fit several pre-hung doors and/or 8' lumber, will *not* fit 4'x8' sheet goods inside).
Dislikes: minor, but we love everything else so why can't they perfect these too? installed TomTom gps is ok but interface is worse than older Mazda installs (no reason imo to seek installed GPS); total of 4 things to reset each gas refill if you want by-the-tank info (how about a 'reset all mileage' choice?); fine on snow but must be more careful than you'd expect on ice as torque is relatively powerful in low gears (we have snow tires)