Other than size (Civic is a compact, Prius is a larger midsize) and styling, be aware that both hybrid choices are different. Honda’s IMA is primarily a gasoline engine with electric assist (the newer HCH II has little electric-only propulsion), while Toyota’s HSD is a full hybrid design that can be gasoline, electric, or a combination of the two. Some people like the simplicity of one hybrid design over another, but that’s a personal choice. Same goes for the instrumentation gages in the HCH vs. the touchscreen in the Prius.

Pricing wise, I’d say go with the Prius.
Toyota Prius, starting at $22,000
Honda Civic Hybrid, starting at $23,650

Hybrids do cost less in the long term than their conventional
counterparts. (Intellichoice used a 5 year ownership comparison in
2006)

While Consumer Reports in 2006 only found the Toyota Prius and the Honda Civic Hybrid would pay off within the same 5 year frame. The Honda Accord Hybrid, the Ford Escape Hybrid, the Lexus RX400h, and the Toyota Highlander Hybrid were also studied. (I’ll note that there was a mathematical error in the initial publication of Consumer Reports’ hybrid vehicle cost analysis, which a retraction was published later… http://www.msnbc.msn.com/id/11637968/ ) Since this publication, many more hybrid models have become available, so I can’t use this to say about hybrids "in general." However, in the
US, the Toyota and Honday hybrids have sold so many that they no longer qualify for the US Federal hybrid vehicle income tax credit, but some some new perks are available from individual states…

Check out the April issue of Consumer Reports if you want reliability information. Both the Honda Civic and Toyota Prius make their best bets for new cars and for used cars.

In the US, hybrid models (like the Prius and HCH II) tend to be the best in fuel economy in their respective classes, using the same testing procedure to compare all cars (hybrid/gasoline/diesel/flex-fuel/etc.), and that is for BOTH highway AND city driving: http://www.fueleconomy.gov/feg/best/bestworstNF.shtml

Toyota Prius: 48 mpg city/45mpg highway/46mpg combined
Owners report average mpg in the mid-high 40s:
http://www.fueleconomy.gov/mpg/MPG.do?action=browseList2&make=Toyota&model=Prius remember that the 2004-current Prius are the same) and
http://www.greenhybrid.com/compare/mileage/toyota-priushsd.html

Honda Civic Hybrid: 40mpg city/45mpg highway/42mpg combined
Owners report average mpg in the 40s:
http://www.fueleconomy.gov/mpg/MPG.do?action=browseList2&make=Honda&model=Civic%20Hybrid (remember that the 2006-current model year are the same) and
http://www.greenhybrid.com/compare/mileage/honda-civicii.html

Both are rated an AT-PZEV in CA emission states, so they have Super Ultra Low Emissions, zero evaporative emissions, plus a long warranty (10 years/150,000 miles) on the hybrid battery in CA emission states. (outside of CA, it’s 8 years or 80,000 miles (Honda)/100,000 miles (Toyota).) (The gasoline-only Civics are only ULEV in comparison.)

The Prius is also in edmunds.com used cars best bets list as well, and their lowest true cost to own list (2007 and 2008).

Both the Prius and HCH are great cars. But, only you can decide which will work out best for you. Take both for a test drive, and see which one you like better, which you like the seating better, and/or like the available options better… Do you prefer a sedan (Honda Civic Hybrid), or do you like a hatchback (Toyota Prius)? Is a compact OK with you (Honda Civic Hybrid), or would you prefer a larger midsized vehicle (Toyota Prius)? If you want a manual transmission, then you’ll have to look for a used HCH. Do you want to show off that you have a hybrid or not? The Prius is only available as a hybrid and its distinctive aerodynamic design gives it away, while the HCH blends in and looks like most every other Civic on the road…

Gets 50 mpg city, 65+ highway.

Blows both of your choices out of the water.

Insurance is cheaper. Cost of vehicle is cheaper.

And no hybrid engine that costs a fortune to fix, everytime it breaks.

Both are quality vehicles and are made right.
IMO, the Prius is a little better because of the synergy technology, which gives it better gas mileage.
The Civic Hybrid is rated at 40 city and 45 highway.
The Prius is 48 City and 45 highway.

Both are excellent in reliability, as most other Honda’s and Toyota.
There is no such thing as a ‘hybrid engine’. The engine is made up of part gas and part electric. Noone has had to replace a battery in any Prius due to failure since it was introduced in 2001.
Even if they did, it is covered under a 7 year, 100K warranty (10 year 150K warranty in CA).

A CRX is a 2 seater that will get you about 50 on the highway max. They are also death traps if you ever got into a serious accident.
In addition, good luck finding one that isn’t a POS since the last year Honda made them was 1991.

You also might try the VW Jetta TDI clean diesel. They get about the same mileage of a hybrid. IDK the prices.