How much are you wanting to spend? You can get a '03-'04 Cobra for around $24k for one that's been babied and has reasonable mileage (<= ~30k). Some decked out premium GTs fetch in the $20s so depending on what price range you are after, definately look into a 03-04 Cobra, if not, a Mach 1 (~$17-20k)
Zero issues with 70k miles on a vert and 40k miles on a coupe (both '03 Cobras), aside from the well known quirks (TSBs) that are easily resolved.
On the non Cobra's, as mentioned the plastic intake is a weak point and I know for sure the V6, maybe the GT also, exhaust header leaks are common (poor factory welds at the flanges).
I'm going to try to list as many negatives as I can, but don't let it deter you. I love my car, but since most responses here will be praise from owners, I'll play devils advocate and cover all the bad things; that most of us don't even care about.
On the Cobra's and Machs (the problem is unique to the DOHC 4v heads) there is a head tick/overheating issue that warps the valve guides in the driver side head but as long as you don't run the car hot and hard all the time or do top speed runs back to back all day under constant boost, it shouldn't surface. There is a cooling bypass mod you can do for about $200 to route the coolant better as a preventative measure. My first Cobra was heavily modified throughout the course of 40,000 miles and didn't have the bypass and never developed the problem, so it's more of a rare thing that causes paranoia for enthusiasts. Creaking steering rack due to out of plane stamped K member that can be resolved with a $30 set of after market bushings, and a squealing throwout bearing retainer sleeve that can be fixed with a $120 stainless steel replacement. These are just common well known problems that CAN come up; the majority of owners live in fear because they want a perfect car and know of the issues, and never actually develop these problems themselves 9 times out of 10.
Misfires are also a recurring problem on the DOHC heads due to the coil on plug design necessitating deep recesses in the valve cover where water can pool; a more pronounced problem on the Cobras due to the heat extractor vents in the hood that dump rain or wash water directly onto the valve covers. Water vapor works it's way under the coil pack cover and into the coil pack recesses in the valve cover, esp in cold weather due to condensation. This seems to be an issue on all the Ford DOHC engines, including trucks, mostly in the rear cylinders due to the engine incline and the fact that the weak point in the coil pack cover seal is at the rear of the valve cover where a grommet allows the ignition harness in to connect to the coil packs. Nothing major, just pull the cover off and blow it out with compressed air and clear the computer code when it occurs.
These are more like known issues that can be resolved if you are aware of them; all cars have their little factory quirks. But other than that, no less mechanically reliable day to day than any other car, import or otherwise.
The Cobra's suspension on the other hand is harsh on public roads and gas, insurance, and ZR rated tires will be recurring expenses.