Idle air control valve was fouled, which required taking apart the throttle body and cleaning that too. Annoying, and from what I read, common. Design flaw.
Transmission shifts harshly. Again, common, there's a TSB on this requiring the replacement of a 200 dollar Honda-only part (linear shift solenoid). Design flaw.
Window keeps coming off the track. Honda's TSB is inadequate as it happens frequently. I will have to replace the window regulator. Design flaw.
Exhaust is not in great shape. Muffler will need to be replaced as well as the catalytic converter due to rust. This may be par for the course, but its somewhat annoying because I've driven American cars in the past which have lifetime stainless exhausts on them.
There is a cold running noise coming from the engine. Again, common, but not well documented as to the cause. Just annoying.
Minor oil consumption. All Civics I've owned save one have had this problem.
I give this car a decent mark for gas mileage. It honestly does quite well and I'm not terribly mindful my driving.
I've owned several Civics: a 1996, 1998, 2003 and this one. They've all had problems. Some I've owned since new and some used. What I mean by problems: things that aren't supposed to go wrong with a car. Brakes, belts, alignments don't count.
I've had two out of four Civics with poorly functioning transmissions.
The '96 had an input shaft bearing go bad, which is a common problem, as well as a failing speedometer which is also documented.
This one has a bad shift solenoid.
The 2003 would have the steering lock up when it was cold (almost ran into a tree because the wheel wouldn't turn).
The 98 had a cracked exhaust manifold.
I don't have anything against the Civic. Any car you buy will have a problem or two. But I've had about as many problems with some of the American cars I've owned. My Jeep Cherokee, for example, probably had fewer problems than any of the Civics I owned.
I think Civics do have their share of problems, and these are often overlooked due to somewhat of a cult following. I think some of the designs are not great (having to remove a motor mount to change the compressor belt?!) and I've been under the hoods of plenty of cars to make the comparison.
You'll notice that I'm still driving Honda. I like the mileage and I've gotten to know the car so I can work on it pretty easily. It's probably about as good as most of the other cars I could be driving. My point is that it's not greatly better than the alternatives. Would I buy another one? Not sure. I liked my Nissan and my Jeep better, to be honest.
My advice is if you have your heart set on a Honda (for whatever reason) buy one and drive it. Have practical expectations about the car, though.