Diesel injector problems (expensive, over £500 to fix).
ABS sensors (£160).
Brakes, suspension, all the expected consumables have been replaced at various services / MOT's.
Air con a bit weaker now.
Bonnet release handle broke off, real pain to get back on, but no big deal.
I keep the car serviced on time and had the timing belt changed (£300). Cosmetically the car is looking a bit rough, but it is now 11 years old.
My grey Octavia 1.6 TDi CR (common rail) Elegance has been my daily driver for a while now and has been an excellent vehicle.
When I bought the car I had heard of the car's legendary popularity and reliability as a taxi, and that influenced my purchase. For the most part the car did not disappoint, however I have had my fair share of running costs and problems as you would get with any car as the age and miles rise (see above faults); however apart from that injector problem, I would say the car has been very reliable. Skoda dealer has been OK with me, but since the car is getting much older, you are better finding a local independent garage for your servicing and repairs, it will be cheaper.
The 1.6 diesel engine is a good one, performance is only fair however. But you will average 60 mpg. I would recommend the old 1.9 diesel or later 2.0 diesel - they do close to 60 mpg as well and have much better performance. If fuel consumption is a concern however, then there is a "GreenLine" 1.6 diesel, that can do more than 60 mpg, but I bet it will be slow. Tax and insurance are also very reasonable - it is the repair costs you have to watch out for with this car, so only buy a looked after car with full history. I have heard the petrol engines are also reliable, but obviously not as good on fuel.
Elegance spec is the one to have - near top of range. The only thing this does not have is heated seats and leather. I believe the top "Laurin and Klement" model has those, but you can get those as an option on the Elegance also. I find my car has enough electronic equipment. Spacious also. Climate control is a bit fiddly and honestly would prefer a simpler system. But try and avoid "S" spec cars, those are lower range and you do not get much. General refinement leaves a lot to be desired - the car is a little bit too noisy sometimes (wind and tyre noise) despite the comfortable seats and equipment levels; it is the only thing that ruins an otherwise pleasant car to be in. Suspension can be a bit crashy and jerky as well, no matter how smooth you drive.
Overall this has been a good car. It is not exciting to drive or anything that will stand out, but if you want a generally reliable practical family car and only have a few grand to spend, check out this face-lifted 2009 - 2012 Octavia.