1. I don't know if your laptop
will overheat when playing FO3, but be sure to keep it on hard smooth surfaces so the vents under the laptop can keep it cool. Even if it means putting a large hardcover book underneath the laptop. You don't want fabrics wrinkling up and blocking the vents. The laptop does have portability, but the desktop would be able to keep cool more easily.
2. If the controller doesn't have a natural USB cord/ plug, you'll likely need a USB adapter of some sort. I've heard numerous people on this board use an XBox 360 controller that has a USB plug to play some of the more recent Bethesda games including FO3. I don't think you need drivers for that one, Windows will likely detect it as plug-n-play hardware and the DirectX DirectInput drivers are likely already installed on your system. Although, maybe some one more knowledgeable about the XBox 360 controller may be able come along and to tell you more.
Myself I actually have a Playstation2 controller plugged into my desktop using an USB adapter I bought from my local Radio Shack, although I'm not sure if they sell them anymore. You could probably buy some online and I've also seen Playstation3 controller USB adapters for sale online. My Playstation2 controller USB adapter didn't require any special drivers to install, although I only use it for racing games.