Is there a clear winner in the filesystem area? As in, does some filesystem perform significantly better in a virtualized environment such as VMWare or VirtualBox? Is there more or less disk space wasted in the VMDK/VDI formats with some filesystems, does the layout of a particular filesystem stand out when running in a virtual environment? Is journalling worth it for non-critical operations? Or are they all the same?
SnapOverflow
Honestly, I've found that my choice of filesystem really depended on what the application of the VM was for. Maybe journaling isn't needed if you're never writing anything (in which case, read only might be in order). I use VMs to experiment a lot and have settled on giving ext4 a try. The delayed allocation seems to work quite well with it though I have no hard numbers to give to you.
So what do you need? Stability and reliability? ext3 might be the way to go. Tons of little files? ReiserFS/ext4(maybe). Large contiguous files? XFS. I would think that anything which can delay writing more will be the most efficient due to overhead in write operations but as of now it's all speculation and theorycraft.
I like VMDK over VDI basically because VMDK is more mature and has more features. I'm not aware of anything VDI can do that VMDK cannot. Both VDI and VMDK support growable disks which saves disk space on the host. But, the maximum size of a VMDK disk can be expanded without having to backup and restore to a new VMDK disk using vmware-diskmanager. You can then use gparted to resize existing partitions to fill the new disk space. Very slick. With VDI, you would need to create a new VDI disk and migrate data from one to the other, AFAIK.
As far as choosing a filesystem on the guest OS goes, I don't think things change that much in a virtual environment. The same properties you use to choose a filesystem apply equally in both cases.