Running the PC via Remote Desktop would almost certainly be faster. Much faster. RD simply pipes the video across to your Mac from your PC. The PC itself is still doing all the number crunching and drive access and such. This will also make your Mac faster since it won't be using up oodles of compute cycles for the emulation. The real PC will also guarantee you compatibility with anything you throw at it. Virtual PC sometimes (although very rarely) has problems with some software titles. Admittedly, though, the only software that ever gave me any trouble was an assembly compiler and debugger for a computer engineering class.
However, this is not to say there are no benefits to Virtual PC. VPC offers drag-and-drop of files directly between your Mac and the PC environments. It also allows you to create virtual network drives on the PC that link to folders on your Mac. Virtual PC gives you the ability to run multiple virtual systems with ease. I, for example, have a Windows 98 setup, a Windows 2000 setup with IE 5.5, and a Windows 2000 setup with IE 6.0. I have the latter two separated for testing web site code in the two browsers. Furthermore, you can pause the PC at any moment and save it for later use. Best of all, since you have a PowerBook, Virtual PC allows you to take your PC wherever you go.
Regarding security, they're the same. Neither is going to hurt your Mac, but both will need the standard PC maintenance.
Remote Desktop is just a window that displays your PC's screen. It's as simple as that. You can interact with it via your keyboard and mouse, but it'll never touch anything on your Mac.
Virtual PC offers a wholly self-contained environment. The emulated PC will never be able to access any of your files unless you explicitly attach some folder as a networked drive as I described above. However, since the emulated PC is practically a real PC for all intents and purposes, you may want to install a spyware scanner or anti-virus software on the emulated PC. Would you put "program X" on your real Windows box to protect it? If so, you should put it on the emulated Windows box as well.
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