Boot and do security checks

I have a few hours to enjoy this days and I did some java code to check some files in my system when I boot up. I'm running a linux distro and I wonder about which are the right checks to do.

By now I'm just checking a few files by hashing them using md5. Files like /etc/passwd or /etc/group

Do you have any ideas? What will you check first?

PD: This checks just take a few secs and prompt a shell with the results.