What's your budget? For under $4k I would go with a ~2002 - 2008 Honda Civic/Accord or Toyota Corolla with a manual transmission. 30+ MPG all day and dead-nuts reliable. Nothing against American cars but from what I've seen the domestic compacts were almost always bought with a slushbox that sucks power and would be expensive to repair if it fails. A Subaru will get you AWD but correspondingly worse MPG (mid 20's for the Subaru vs mid 30's for the Honda/Toyota.) Mazda and Nissan can also be found with manual transmissions.
Sadly, I sold my MT 'commuter' car (a 2002 Nissan Pathfinder) in December after I crunched the numbers and realized it was stupid for me to have a "commuter" vehicle when my commute totals 60 miles a week (I work at home 2 days a week and on the other 3 days my commute is only 10 miles one way.) The Pathy was a nice vehicle but it really didn't get very good MPG (16 - 17 though that was still better than the Suburban's 10 - 11.)
I miss having a manual transmission car but grudgingly admit that my gas pig Suburban does fine hauling my butt to and from work.
German cars - Audi and VW mostly - seem to offer good MPG but people seem to either absolutely love them or absolutely hate them. I guess some German cars have lots of finicky electronics that can get buggy? Dunno, the only German vehicle I've ever owned is a BMW motorcycle and it still runs fine.
EDITED TO ADD: Some Subarus with the 2.5 engine have head gasket issues. I had a '99 Outback wagon and had no problems with it, and pretty much everyone in my family owns a Subaru, so far none of them have had any issues. I sometimes think the Internet "squeaky wheel" syndrome magnifies flaws and makes people think there are more problems than there actually are, nevertheless, it is something to be aware of as a head gasked is a ~$3000 repair on a Subie.





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