This is something I'm keenly interested in.

For two years now, I've been using or tinkering with Virtual PC, VMWare Server, VMware Player, and Virtual Box.  I still haven't found one I'd call "the best".  They each have significant pros and cons.  I really want to like Virtual Box.  It's getting better (12-18 months ago it was unstable and completely unusable for my needs), and I think it might have the best potential, but for me it's not there yet.  Virtual PC continues to be my default choice for most purposes.

Virtual PC let's you "insert" a virtual CD simply by dragging and dropping a iso image onto the CD icon in the system bar.  Ditto for images of floppy disks.  Drag and drop a different iso and you've just swapped CDs.  It can't possibly get any easier!  In contrast, Virtual Box makes you open a dialog box, unmount the existing iso image, browse to the replacement image, remount, and close the dialog box.

I find it's also easier to move files between guest and host with Virtual PC--just drag and drop into the vm window.  With VBox or VMware I need to setup networking between the vm and the host, then transfer via common networking methods.  (I think you're supposed to be able to drag/drop between windows, but it's never worked consistently for me.  I'd end up pulling out my hair if I didn't setup networking.)

I also can't live without VPC's "Undo disks".  This feature let's you drop everything done in the current session, so next time the vm will start just like the last.  This is extraordinarily useful when websurfing.  VBox and VMware have snapshot features, but you have to have the foresight to manually take a snapshot, then have to manually revert to the snapshot.  It will do a similar job, but isn't as convenient to use as VPC's Undo disks.  Snapshots are a "erase-what-I've-done-and-restore-previous-state", while Undo disks are "don't-bother-saving-this-in-the-first-place."

Undo disks also makes it extraordinarily easy to test new software.  If I want to just see what a new program does, I open a Windows vm, drag and drop the installer on the vm's desktop or drop an iso onto the virtual CD drive, install the program, check it out, then shut off the vm, without saving anything from that session.

There are other differences, but these are some of the most significant to me.

The big problem with Virtual PC is its lack of USB emulation.  If I need USB, I have to use one of the others.  But for me, that's not that often.  Note that a USB mouse or keyboard is not a problem--the host's USB kybd/mouse controls the standard emulated kybd/mouse in VPC.  Same with USB hard drives and USB network adapters--they're shared by the host, not seen as USB devices in the vm.  I network my printers, so those have never been an issue with VPC.

But for devices like USB scanners, digital cameras, and camcorders, I currently use VMware.  VMware is not very convenient because I have to use both Server and Player.  VMware Player does not let you create virtual machines or swap virtual CDs, but VMware Server has a heavy footprint and does not coexist peacefully with the others.  Coexistence is essential because none of these vm programs is perfect enough to preclude using another.

I currently use a mix of true multibooting and virtual machines.  I now use virtual machines for much of what I used to multiboot for, resorting to multibooting only when a vm won't do.  I use a multiboot partition with VMware Server installed so I can create vms, and another multiboot partition with everything else.  Vms created with VMware Server can be played with VMware Player in the other multiboot partition, but it's that particular reason for dualbooting I'd like to eliminate with Virtual Box.

But I haven't made that jump yet.  One irritation is my old VBox vms don't play in the current version of VBox, and I haven't gotten around to rebuilding them from scratch.