The ZF Tiptronic transmission used in the pre-facelift 996s is a fairly robust unit, and they don't seem to suffer from many problems. It was a £3300 option in 2000, but that doesn't relect in the price of used cars - they are fairly equal in value comparing like-for-like. Manual transmissions are fairly robust too, but they can suffer from 2nd gear syncho wear. I suspect this is caused by impatient owners being a bit ham-fisted when the car is cold, as the 1st-2nd change can't be hurried until the gearbox is warm. As Martin says, you don't have the clutch issue with a Tiptronic!
Martin is also probably correct about desirability, but it all depends on how you are going to use the car, and which you prefer. Tiptronic is perfect for my usage - a cross town commute every morning - but I drive it in manual mode all the time, because I like to choose which gear I am in. When poodling in auto it tends to change up too quickly for my liking. On the open road it is a lot of fun too, and I can honestly say I don't miss the manual change. All my cars prior to Porsches were manuals.
The best thing to do is to try it, and choose what YOU prefer. If you are planning to keep the car for some while, it won't make a big difference to the resale price. You may love Tip or hate it, and there are as many people who love it as those who don't. Hence why they sold in roughly equal amounts. If you do get a Tip with around 70k on the clock, budget for a fluid and filter change though - see the other recent thread.