I would highly recommend taking a look at the Mazda3, Honda Fit, Honda Civic and possibly the Scion xD. All of them are reliable, safe, economical (28+ mpg) and relatively nice to drive.
The Mazda3 is my personal favorite. For $10k, you could easily find a nice 2nd-generation (2010-2013) model. The 2010-2011 with the standard 2.0L engine averages about 28mpg and the 2012-2013 with the 2.0L "Skyactiv" engine ups that to 32mpg.
The Honda Civic and Fit are both great cars, but the Fit is my favorite of the two. I like the hatchback versatility and the car's design (the seat-folding configurations, space utilization, etc.) are ingenious. It's the more economical of the two, but either one is great on gas and rock-solid reliable.
I mention the Scion xD since you are already a Toyota owner. The fuel economy and reliability are competitive with the other cars I mentioned, but it isn't quite as nice as they are. Still, it's a solid choice if you're wanting a Toyota product.
Of the cars you mentioned, I would strongly recommend that you avoid the Nissan Versa, Ford Fiesta/Focus and VW Beetle. The original Versa (2007-2011) was actually a pleasant little car in most respects, but it has not been reliable over the long haul. The current Versa (2012-present) is just a cheap, noisy, slow and generally unpleasant vehicle. It has also been less than reliable.
The Ford Fiesta and Focus are also very likable cars on the surface. But reliability issues have plagued both cars from day one, particularly problems with the automatic transmission. If you are considering a manual transmission, they might be worth a look, but that would be the only exception.
The VW Beetle is slightly more reliable that the other three, but nothing like a Honda, Toyota or Mazda. The year models that would be in your price range typically have the 2.5L 5-cylinder engine, which isn't very fuel efficient.
As for the Toyota Yaris and Prius, I'm just not a fan. The Honda Fit is exponentially better than a Toyota Yaris of the same year model. It's not that the Yaris is that bad, just that the Fit is that good. The Prius is purely a personal prejudice- I just don't care for them.