So far I have seen very few issues - which is why I have ordered a Mac Pro myself.
1. I've seen one report of a DoA
2. A handful of people have had to re-seat the memory risers after delivery.
3. One report of an overheating 7300 video card - probably a manufacturing defect.
4. Some reports of instability that can be resolved by reinstalling the OS from the DVD supplied - apparently the build on some shipping machines is earlier then that on the DVD.
5. Some reports of software instability caused by migrating software from other Macs.
6. One or two people reporting excess noise from one of the fans - replacment required.
7. Some people finding the system slower than they expected - usually due to a combination of running software under rosseta with only 1 GB of memory. Possibly made worse by Spotlight indexing at the same time on out-of-the-box systems.
Just a few issolated issues. Vast majority of people sound happy.
Two points to note...
1. Some issues getting SATA drivers to install for Windows XP. A work around has now been found to this. By the time the final version of Bootcamp is released as part of Leopard I expect this will have been resolved.
2. Late in development of the Woodcrest Xeon CPUs Intel (or more exactly the manufacturers who had been given samples of the chips) found some problems with using the CPUs in conjunction with hardware RAID support build into the support chipsets. Possibly as a result, Apple does not make use of the hardware RAID option in this version of the Mac Pro. Later revisions may use this feature once it it working - but I doubt the revision A will be able to "activate" the feature. That is of course pure speculation and I don't see it as a reason not to get what otherwise looks like an excelent machine.
Of course it is too early to say what kind of long-term problems may exist. However given the relativly untroubled history of the Intel-powered iMac and Mac Mini it looks like Apple have done a good job on their desktop systems.