Vee-dub TDI would be an attractive option if most of your commute is freeway.
A used Fit (auto trans) would be another option that is much more Japanese. And you can likely get that for less than your budget. It's a little wagon, so it can haul a half-decent amount of stuff as well. The manuals are not as good as the autos for FE because the gearing in the manual trans is shorter than that of the auto. (WHY, HONDA, WHY???!!)
For new cars, there are several Hyundais that are EPA rated at 40 MPG on the freeway test. Pretty decent numbers, there. They're Korean, not Japanese, but I'm guessing there isn't a huge amount of difference at this point.
-soD
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