First, read the this thread as it explains in detail the difference between Virtualisation and boot camp and why you would want one over the other.

The applications are very similiar. Parallels tends to have more utilities devoted to bridging the gap between the OSes. It has utilities to browse the virtual machine from the mac, and will also make PC applications show up in "open with…" menus on the mac side and Mac apps show up on the PC side so you can open any file in any program from either OS. VMware fusion tends to concentrate on simply the emulated environment. I personally prefer VMware because it seems less invasive when installed on your system (I don't want all that bridging) and because it has a few perks Parallels lacks (Bluetooth support is one that is key for me). Also, if you happen to be visually impaired, do not buy Parallels - it uses non-standard interface elements that VoiceOver can't interpret (very annoying).