Eugene,
It depends on your budget - i.e. year of production you can afford.
Some of the options on early models (01-02) became standard on '03 cars, but the most sought after items seem to be Sat Nav, Cruise Control and Park Assist.
Beyond these, it tends to be the more personal items such as ruffled leather seats (as my wife said, made from cows with cellulite...) , Bose sound systems, Chrome pack and electric memory seats. The last item is good if you intend to regularly share the drivers seat with others - which is why I don't have it...
Known faults? Not many - the turbo, coming into production 2 years later than the normally aspirated 996, seems to have avoided the production problems that were found on some 98-2000 cars. It's also very different in many ways to the standard 996.
It costs a bit more to service, but it's generally acknowledged as a reliable car. Other contributors to this forum may have something to add here.
Otherwise look for one that has a tracker already fitted (will be almost essential for insurance and will save you £500+ to have fitted), and ideally the original or extended warranty still in force.
Seems to be a good time to buy - there'a lot for sale on Autotrader (96), through the OPCs and the independents.
Matthew