IT is running a series of VMs that we'd like to see optimized further: if the VMs' are Windows XP, storing their NTFS images out to the virtual disk (ext3) provided by Linux/VMWare, how much of a hit are we taking - as opposed to having a partition of the host hard drive formatted NTFS to eliminate the translation layer and the extra level of operating system IO preparation?
Chopper is correct. Using ESXi or ESX with VMFS formatted datastores, virtual filesystems only drop by 2-3% in performance when compared to the same filesystem running native on the same hardware. Using VMware Server this performance drop increases due to performance overheads incurred by the host OS outside of VMware's control.
At the end of the day I find that the benefits of virtual drives far outweigh the very minor perfomance drop incurred. VMotion for example.
These are all observations I have made through years of use and actual benchmarking. As sascha states talk to the VMware experts to get accurate, rather than assumed, advice.
You are probably losing some performance by using a virtual disk, so the fastest way would to have a separate drive. Another way would be to have a separate partition on the main drive formatted as NTFS. This is definitely faster than a virtual disk, but it is slower than a separate drive.
This would be better asked over at the VMware Forums where you can get the advice of people who do this kind of performance tuning for a living. You're not going to get any hard numbers about how much of a hit you're taking here :)