The safest option is to buy the car from Porsche (OPC), since you will then get a 12 months warranty.
Additionally you can extend the warranty each year upto 120K miles or 10 years, subject to getting it serviced by them (or getting an annual inspection by them).
Note that the warranty will not cover the clutch or brakes.
The clutch costs about 1K to replace by OPC, and they will not give any guarantee, so it could fail a week after you get the car. There is no easy way to tell how much life is in it.
(The clutch has quite a distinctive feel, since it is hydraulically operated - there is no cable. This was done to make it easier to press the pedal since the springs are pretty strong to take the torque. If you go for the manual you will stall it lots when reversing, till you get used to it[
]).
Brakes (discs) you can get checked out, or ask the OPC how much life is in them.
For RMS, the bottom end of the engine is the same for 996 (C2, C4, C2-cab, C4-cab, C4S, C4S cab, targa) and new 997 (C2, C2S). It is also the same for 986 and 987.
It was a new "clean-sheet" design for the watercooled cars.
It was intended to be lighter, stronger, easier and cheaper to manufacturer.
The turbo engine has little in common with the normally aspirated cars. It is a blown GT3 engine without the titanium conrods (although if have the money these can be added, then the rev limit can be raised which gives a top speed over 200).
The GT2/3 and TT have different bore diameter and strokes. The bores are "Nikasil" treated (which is expensive) whereas the other cars are produced "Lokasil" process. This was a new process developed by the KS company in cooperation with Porsche.
You do not need to worry about most of the issue raised on the other cars.
PCM is CD-ROM based. Porsche are no using a DVD based system.
As various other threads have pointed out, it seems there are no upgrade discs available (so the M6 toll road does not exit, for example).
There may be some upgrade for the first cars, but in general even with the latest ones the maps are not 3-4 years out of date.
For non turbo cars, the 993 may be more valuable than the 996, partly due to rarity value as anything else - it was made in much lower numbers.
For turbo cars, I think the same will not be so true. The turbo cars all have their own unique character, and the 996 is good enough to stand on its own.
Condition and mileage will be the main deciding factor on the price.
Although I reckon too low miles and infrequent usage are worse than regular usage.
If you buy a 3 or 4 year old car, then in 3 years it will be 6 or 7.
What will this be worth - it was a 90K car new, so is 50% reasonable? I think it may well be lower, since the car is just not rare enough.
There is increasing competition coming.
In 1-2 years time you may have some 400-500 bhp cars from the Japanese manufacturers. 1-2 year old 2nd hand cars from them may tempt people (Nissan and Toyota are pretty reliable).
Some people defected from the 996TT to get Lambo Gallardos. Not sure what their prices are doing.
Anyway, don't sell, then depreciation is not an issue.
Drive it as much as possible - there is no point saving it for someone else.
Mine's 14 months old, and has done more than 21K miles.
I don't intend to sell. In 5 years time I might buy something else, but it will be in addition to, not instead of.