First off I wouldn't recommend running the same Windows installation both natively and virtually. The hardware differences between the VM and the real machine tend to throw Windows into a bit of a tizzy to put it mildly.
Keep your current Windows installation for native use, and create a new installation within a virtualization product for running within Ubuntu.
I personally use VirtualBox and would recommend it every time. I used to be a big fan of VMware, but VirtualBox has just got the edge because it is so much more open than VMWare. Even VMWare's "free" products seem somehow restricted and clunky by comparison. Ever since VMWare Server (which is what I used to use all the time) went to having a web based front end I have had no end of trouble with it, and it just refuses to work on some operating systems (you have to apply patches to get it working with Ubuntu).
QEmu I don't even place in the same class as VirtualBox and VMWare. While it has its uses (I use it to test-boot my software distro) the performance and usability is well below that of VirtualBox.
Make sure you use version 4, not the older version 3 that is in Ubuntu main. You will have to go to the VirtualBox website and add the repository to your apt sources file or download it manually. I prefer to add the repository as it does updates for you then.