I doubt you really wanted to read all of this when you thought to ask, but here it goes...
Civic Si: Leaking differential, three really bad rattles behind interior panels that couldn't be fixed, seats that were worn in the butt area with only 5,000 miles in both front seats, front passenger suspension clunk. Traded at 6,000 miles, stupidly, for an '09 Accord V6 EX-L coupe with every single option.
Accord (brace yourself): all four wheels dried with paint drips that were broken off down to the metal, panels fit together so poorly that the tail lights pushing against the body chipped the paint in three places, crooked body panels including the trunk and hood that had to be loosened and straightened by the dealer body shop, interior roof trim hung down on one side where it didn't even stretch all the way across (right?), driver's seat had to be removed and the power motors and drive mechanism replaced as well as the tracks they were on, passenger seat came with two of four bolts missing that held it to the floor (right?), two really bad pops on every single bump from the console and dash trim around the stereo, *here's where it gets ugly* the VCM that turns cylinders off would bind the engine on the interstate and buzz loudly and vibrate the car until I pushed the gas down to force it into 6 cylinder mode, torque converter that kicks in and out when VCM changes mode would make the car surge constantly even on level ground at steady speed, and finally, the transmission would jerk the car badly on a very small grade at the end of my street going away from a stop sign every single morning until it warmed up.
There were actually other issues that I cannot remember with the Accord, but holy crap that car was a lemon. I traded it with about 5,500 miles for my '09 Mazda 5 GT with Navi, remote start, Sirius, etc. Loaded. I love the Mazda. Both Hondas I did probably lose $500-$1000 combined since I got extremely good deals and the resale is great. I also got my 5 with a $26,900 MSRP for $21,500, so I tend to get really good deals because I'm a hustler when it comes to cars. Dealers like when I finally leave. I play them like they wish they could play me.
Now, that said, I just bought another Civic Si. I bought one of the very last ones before the new body style. The '09-'11 had several changes that my '08 didn't have so most gripes where improved. I got $4K off the sticker and can bail out if I have any serious issues and actually profit. So far, at 3,000 miles I don't have a single problem with it. That's my Honda story. I would watch the Accords very, very closely before I ever bought another. I ordered mine though so I had to take what I got. Never again.