ive seen in the services that you can have a delayed start up, but i dont think you can have a delayed start for normal programs, just pin them to the taskbar and start them when you need them.
If you know scripting a bit, just get Windows Server 2003 Resource Kit Tools, create a batch (.bat) file containing the command you want to run and add the "sleep" command before it. Call that batch file from the registry instead of your command directly.
It can auto start apps at a certain time after startup, anytime you want it to. or even run stuff on shutdown.
If you use it for a startup item it will close 30 seconds after its done starting stuff.
I use it to tell my server to shut off my computer when it powers off since it only powers off when i get an extended power out(UPS tell it to shut off and it tells my computer to shut off).