Given the similarities in features and performance between these two programs, deciding on one or the other isn't easy. If your needs include gaming in virtual Windows installations, Parallels is the preferred option. Similarly, Fusion is the one to get if you love experimenting with lots of different virtual OSes, thanks to VMware's huge library of ready-to-run OS "appliances."
Beyond that, it comes down to some little things. Fusion, for instance, manages app windows better than Parallels, while Parallels offers better gaming and 3D performance.
There is the issue of cost. At this time, Fusion 5 is selling for $50 (no upgrade pricing), and Parallels for $80 (or for $50 if you're upgrading from an earlier version or "crossgrading" from Fusion). More significantly, Parallels uses a per-machine license. A two-license version is $100, but you'll need licenses to cover each Mac you use. Fusion, on the other hand, allows one license to cover as many Macs as you personally use. So if you're in a multi-Mac household, Fusion could save you a bunch of money.
Still both are excellent programs, and you can't go wrong either way. Thankfully, both have free trials available, so you can download and try them out to see which works best for you.