Though I only have firsthand experience with everyday use of parallels, I would recommend Fusion.
Here's why:
Though credit needs to be given to Parallels for being first to market, they are a smaller organization (with less support).
I purchased Parallels 2.5 with a promise for a free upgrade to version 3. Then, version 3 came out and Parallels retracted their offer and decided not to make it free. Also, Fusion is now saying that their next upgrade will be free.
VMWare has a much longer history with virtualization and also more resources.
From the reviews that I have read, Fusion is also not as RAM hungry and less intensive on the processor.
So, having been a Parallels user with no firsthand experience of Fusion, I still vote for Fusion as being better.