Well if he had physical access to your computer, and he's computer savvy like you said he is, I doubt you will know.
You could check to see what programs and processes are being used in your Windows Task Manager (press CTRL + ALT + DEL keys together).
And if you click on the "Processes" tab, anything that looks strange, do a search on that program to see if anything comes up and what others are saying about those programs.
Since your dad had physical access to your computer, it's very easy to install a spyware program and have whatever security programs that prevent spyware from running, to be circumvented.
I'm sure your dad is looking out for your best interest. If you were a father, would you not want the same and look over your own children?
You can always sit down and ask your dad openly and see what he says. Perhaps he just sits down to use your computer and sees whatever you got laying around in your computer.
Good luck!