A comparison of the two could easily fill a whole article. Microsoft Virtual Server 2005 R2 is available as a free download (although you obviously need to have paid for any licenses for the OSes to be run in it), as is VMWare Server. One big difference between the two appears to be ease of use: Virtual Server requires a little more work to get up and running and work with, while VMware is more wizard-driven and that much easier to get a handle on.
The other difference seems to be performance, but this is debatable. I have read a few newsgroup postings that seem to indicate that Virtual Server is slightly faster with regard to some I/O operations. Most people don't seem to be able to find any real difference between the two that would motivate them to switch from one to the other. (If you've used one or the other already, you will probably be inclined to stay where you are.)
Dig Deeper on Microsoft Hyper-V and Virtual Server
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