If you have a router then you could network the two computers together. Or you could buy a crossover cable and network the two with out a router..you would have to disconnect from your internet while you did this though.

File are fine for transferring. Programs on the other hand will have to be installed on the new system due to the way they interact with the registry.

The files and setting wizard will work fine if you have a CD/DVD burner or even better USB thumb drives..it will load all the files and setting from your old system onto the media you choose then you just transfer that over to your new system..But if you are running two different OS's then you more than likely will only be able to use the files as the settings section..ie desktop layout colors etc would be different.