To make it more clear, you'll use what's called Target Disk Mode. Connect the two computers via FireWire, and restart one of them (the one you're transferring from would make more sense in this case) while holding down the T key on the keyboard. It will start up with a FireWire logo bouncing around on the screen, and should then also appear on the desktop of the other Mac. Actually, if you do this before you've set up the new Mac, you can use Migration Assistant right at the beginning to transfer settings and user files as well, if you want, or if you don't want that, you can still use it to transfer the applications. If you want to do it manually, that will depend on the software, as some applications make it difficult to drag-and-drop from one computer to another via license files or other hidden support files.
jW