Munyard,
Applications are usually done by MSI packages or setups with answer files these days. http://www.appdeploy.com contains a lot of information for lots of different applications. This appliance is geared toward OS deployment. I'm not an application expert, but that's where I would start. You can create your own MSI installs with software like WISE studio http:/www.wise.com but beware: its not as easy as it sound from this post... Good luck!