There are non-journaling file systems that you can use in Linux. Journaling file systems would only tend to slow it down if it has to do a lot of writes or renames. If it's just an OS, sitting there idle, that may be fine. If it's a file server, that should be fine as well. If it's a mail server, however, you may want a non-journaling system to handle the queues and the messages being processed through them...so it's kind of server-function dependent. Just keep in mind that non-journaling systems are older and more robust because of how long they've been in service (think proven.) Journaling systems are newer, but have the advantage of performance when you're dealing with larger files.
The beuty of Linux is that you're not stuck with NTFS or FAT32... You can go with EXT3, Reiser (not for long...I think there's a lawsuit), or a number of others. Try EXT2 if you want to try a solid non-journaling file system.
The real question is what version of VMware are you dealing with? If you're running workstation, you're not going to have the same level of control over the physical hardware as you would if you were running ESX 3 Server. ESX 2 is also slightly more limited because of the VM Kernel design.
Stepping away from the file system, the basic elements of each OS are going to be different. Linux boxes can run a lot of services. Depending on the Windows OS and what services you are running by default on each OS, they can be really different. If you're doing any Directory Services or Time Syncronization, this adds to the per second processor time needed and it really makes the VM Kernel's job of splitting CPU time more of a task.
