We are using a WinPE environment that is booted into via PXE from a Windows Deployment Server. I am wondering if there is a way for us to copy registry information and files into the WIM file that we boot from so the applications are already installed and registered? Or will I need to script the installation and registration to occur each time we boot into WinPE?

Customizing WIM is a complex task, however it can be done, here is a documentation from Microsoft on Windows AIK:
http://www.microsoft.com/en-us/download/details.aspx?id=2458

To do it, run in "Windows PE console" something like this:

  1. Mount WIM:
    Dism /Mount-Wim /WimFile:D:\ABoot\iso\sources\boot.wim /index:1 /MountDir:D:\!
    
  2. Attach Registry from a file to your local registry, add your values, unload registry:
    reg load HKLM\my D:\!\windows\system32\config\software
    
    reg add "HKLM\my\Microsoft\Windows NT\CurrentVersion\Fonts" /v "Courier New (TrueType)" /t REG_SZ /d cour.ttf
    
    reg unload HKLM\my
    
  3. Unmount WIM:
    Dism /unmount-Wim /MountDir:d:\! /Commit
    

Another and an easy way is to add user's script in Boot Disk Creator while preparing bootable media, This script is automatically launched when WinPE is loading. This is how to do this: http://boot-disk.com/booting_disk_drivers.htm