FBA Run/RunOnce/RunOnceEx commands may help you with it (please look at XPe
docs).
You may also do your custom shell if you don't need Command Prompt or
Explorer shell in your image. Then you app(s) can be launched as the custom
shell (please also take a look at XPe docs).
Also, you can set the following registry values directly (choose one
depending on your needs):
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnce]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnceEx]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon]
"Userinit"
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon]
"Shell"
(MSDN has all info about these keys).
In case you have Explorer shell you can also setup "Startup" items.
In you have Command Prompt, you can run your apps from a batch file that
gets run by the shell from command line arguments (take a look at Command
Prompt XPe component).
Hope this helps,
KM