One of the annoyances with certain applications is that you need to restart them when you reboot. Most applications that need to be on all the time are smart enough to reinitiate when you reboot or give you the option for them to run at startup. Others like Viigo do not have this option.
Summer let me know that ShaoSoft released the free Start Me Up application to solve this exact problem. You can set what applications you wish to starts and then wait a few seconds before rebooting. You can even set a restart delay so that applications will only fire up 30 seconds after the reboot so that the device is already connected to the internet and initiated.